Contacts of the helix formed by residues 53 - 80 (chain B) in PDB entry 1XIL
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 53 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B ALA* 3.0 16.6 + - - +
51B LYS* 3.2 12.7 - - + +
52B GLY* 1.3 72.1 - - - +
54B VAL* 1.3 57.8 + - - +
55B THR* 3.4 10.0 + - - -
56B ALA* 3.0 34.0 + - + +
57B GLN* 3.0 32.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 54 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B GLY* 3.1 13.4 + - - +
53B ASP* 1.3 72.7 + - - +
55B THR* 1.3 66.8 + - - +
57B GLN* 3.3 17.1 + - + +
58B ILE* 3.0 43.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 55 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B ASP* 3.3 7.7 + - - -
54B VAL* 1.3 79.4 - - - +
56B ALA* 1.3 58.2 + - - +
58B ILE* 3.3 6.9 + - - +
59B ALA* 2.9 31.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 56 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B ALA* 3.8 14.4 - - + -
53B ASP* 3.0 32.5 + - - +
55B THR* 1.3 75.0 - - - +
57B GLN* 1.3 67.6 + - - +
59B ALA* 3.3 7.5 + - - +
60B LEU* 3.0 32.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 57 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B YOF 2.8 69.2 + - + +
48B ALA* 3.9 14.8 - - + +
49B LEU* 3.8 23.5 - - - +
52B GLY* 4.3 4.5 - - - -
53B ASP 3.0 28.8 + - - +
54B VAL* 3.6 18.2 - - + +
55B THR 3.2 0.2 - - - -
56B ALA* 1.3 77.2 - - - +
58B ILE* 1.3 63.7 + - + +
60B LEU* 3.2 9.7 + - - +
61B GLN* 3.4 11.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 58 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B VAL* 3.0 37.2 + - + +
55B THR* 3.9 5.4 - - - +
57B GLN* 1.3 76.7 - - + +
59B ALA* 1.3 63.2 + - - +
61B GLN* 3.1 42.2 + - - +
62B PRO* 3.6 4.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 59 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B THR* 2.9 22.1 + - + +
56B ALA* 3.7 8.1 - - - +
57B GLN 3.3 0.2 - - - -
58B ILE* 1.3 77.5 - - - +
60B LEU* 1.3 60.7 + - + +
61B GLN 3.3 0.2 - - - -
62B PRO* 3.5 12.8 - - - +
63B ALA* 5.2 1.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 60 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B THR* 3.9 15.9 - - + +
44B LYS* 3.8 36.1 - - + +
45B YOF 3.7 45.8 - - + +
48B ALA* 4.4 4.5 - - + -
56B ALA* 3.0 25.5 + - + +
57B GLN 3.6 6.1 - - - +
58B ILE 3.1 0.6 - - - -
59B ALA* 1.3 77.5 - - + +
61B GLN* 1.3 66.4 + - - +
62B PRO* 3.4 1.3 - - - -
63B ALA* 3.2 11.7 + - + +
64B LEU* 3.0 21.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 61 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B YOF 5.0 12.8 + - + -
57B GLN 3.4 14.7 + - - +
58B ILE* 3.1 34.8 + - - +
60B LEU* 1.3 76.4 - - - +
62B PRO* 1.3 67.1 - - + +
64B LEU* 3.2 6.5 + - - +
65B LYS* 2.9 27.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 62 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A GLN* 3.8 19.3 - - - +
58B ILE 3.6 5.6 - - - +
59B ALA* 3.5 17.3 - - - +
60B LEU 3.5 0.4 - - - -
61B GLN* 1.3 93.6 - - + +
63B ALA* 1.3 57.3 + - - +
65B LYS* 4.1 7.9 - - + +
66B PHE* 2.9 32.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 63 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A GLN* 4.0 10.0 - - - +
41B THR* 3.7 22.0 + - + +
59B ALA 5.2 1.1 + - - +
60B LEU* 3.2 13.4 + - + +
62B PRO* 1.3 80.8 - - - +
64B LEU* 1.3 58.2 + - - +
67B ASN* 2.9 47.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 64 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B LEU* 3.6 29.8 - - + -
41B THR* 3.8 19.4 - - + +
42B GLU* 4.3 15.9 - - + +
45B YOF 5.4 11.7 - - + -
60B LEU 3.0 16.9 + - - +
61B GLN* 3.7 6.7 - - - +
63B ALA* 1.3 74.7 - - - +
65B LYS* 1.3 61.0 + - - +
68B GLY* 2.7 33.9 + - - +
69B GLY 3.9 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 65 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B GLN 2.9 16.5 + - - +
62B PRO* 4.1 6.1 - - - +
64B LEU* 1.3 80.6 - - + +
66B PHE* 1.3 57.0 + - - +
69B GLY* 2.8 29.1 + - - +
143B GLN 3.9 2.8 - - - +
144B ASP* 2.9 44.0 + - - +
145B PRO* 4.3 10.7 - - + +
149B THR* 4.4 12.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 66 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A GLN* 3.8 49.4 - - + +
120A GLY 4.4 0.2 - - - -
34B PHE* 3.7 22.9 - + - -
62B PRO 2.9 19.3 + - - +
63B ALA 4.1 0.9 - - - +
65B LYS* 1.3 78.7 - - - +
67B ASN* 1.3 74.9 + - - +
70B GLY* 2.9 22.5 + - - -
142B ASN* 4.8 4.0 - - + -
143B GLN* 3.2 28.7 - - + +
144B ASP* 5.8 0.7 - - - -
161B TRP* 3.6 39.0 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 67 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A GLN* 4.8 2.2 - - - +
34B PHE* 3.4 40.3 - - - +
37B ASN* 3.3 36.6 + - - +
38B LEU* 3.8 15.0 - - - +
63B ALA* 2.9 38.4 + - - +
66B PHE* 1.3 88.8 - - - +
68B GLY* 1.3 60.6 + - - +
71B HIS* 2.9 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 68 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B LEU* 3.8 24.9 - - - +
64B LEU* 2.7 25.0 + - - -
67B ASN* 1.3 74.9 - - - +
69B GLY* 1.3 60.5 + - - -
71B HIS* 3.3 3.6 + - - +
72B ILE* 2.9 33.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 69 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B LEU 3.9 0.2 + - - -
65B LYS* 2.8 19.8 + - - +
68B GLY* 1.3 71.2 - - - -
70B GLY* 1.3 55.6 + - - +
72B ILE* 3.2 2.1 + - - +
73B ASN* 2.8 34.9 + - - +
143B GLN 3.2 23.3 - - - -
145B PRO* 3.8 20.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 70 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B PHE* 3.7 18.6 - - - -
66B PHE 2.9 19.8 + - - -
67B ASN 3.3 1.5 + - - -
68B GLY 3.3 0.4 - - - -
69B GLY* 1.3 74.2 - - - +
71B HIS* 1.3 62.4 + - - +
74B HIS* 2.7 33.1 + - - +
143B GLN* 3.5 19.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 71 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B HIS* 3.9 19.5 + + + +
3B SER 3.3 27.1 + - - -
5B PRO* 4.1 2.2 - - + -
31B HIS* 2.8 32.7 + - + +
34B PHE* 3.9 5.6 - - + +
35B VAL* 3.6 10.8 - - + +
38B LEU* 3.6 27.1 - - + -
67B ASN 2.9 18.0 + - - +
68B GLY 3.6 3.6 - - - +
70B GLY* 1.3 76.2 - - - +
72B ILE* 1.3 65.6 + - + +
75B SER* 2.8 47.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 72 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B GLY 2.9 23.2 + - - +
69B GLY* 3.6 4.9 - - - +
71B HIS* 1.3 80.3 - - + +
73B ASN* 1.3 72.8 + - - +
75B SER* 3.8 4.4 - - - -
76B ILE* 3.1 41.6 + - + +
145B PRO* 4.1 27.1 - - + -
146B LEU 5.8 0.7 - - - +
154B PRO* 5.9 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 73 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B GLY 2.8 19.9 + - - +
70B GLY 4.1 0.2 - - - +
72B ILE* 1.3 75.8 - - - +
74B HIS* 1.3 61.0 + - - +
76B ILE* 3.3 4.3 + - - +
77B PHE* 2.9 26.9 + - - +
123B TRP* 3.5 36.8 - - + +
125B TRP* 3.9 20.9 - - + -
143B GLN* 3.0 48.3 + - - +
144B ASP 4.1 2.8 + - - -
145B PRO* 3.4 22.2 - - - +
146B LEU 4.4 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 74 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B HIS* 3.2 23.9 - + - -
30B HIS* 5.1 0.2 - - - +
31B HIS* 3.6 24.5 - + + +
34B PHE* 3.4 26.1 - + - -
70B GLY 2.7 28.2 + - - +
73B ASN* 1.3 75.2 - - - +
75B SER* 1.3 65.3 + - - +
77B PHE* 3.2 5.1 + + - +
78B TRP* 3.1 43.8 + + + -
123B TRP* 3.6 9.1 - + - -
143B GLN* 3.5 20.6 + - - -
159B ASP* 3.5 2.0 + - - -
163B HIS* 3.9 0.4 + - - -
600B MN 2.2 36.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 75 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B PRO* 3.8 10.0 - - - +
31B HIS* 3.4 16.9 - - - -
71B HIS* 2.8 39.0 + - - -
72B ILE* 3.8 4.7 - - - -
73B ASN 3.3 0.2 - - - -
74B HIS* 1.3 76.3 - - - +
76B ILE* 1.3 63.8 - - - +
78B TRP* 3.7 11.0 + - - +
79B THR* 3.4 19.9 - - - +
192B ARG* 5.1 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 76 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B ILE* 3.1 32.6 + - + +
73B ASN 3.6 5.8 - - - +
75B SER* 1.3 76.0 - - - +
77B PHE* 1.3 66.6 + - - +
79B THR* 2.7 20.4 + - - -
80B ASN* 3.0 30.2 + - - +
125B TRP* 3.9 22.0 - - + -
154B PRO* 3.5 32.5 - - + -
155B LEU 5.0 0.7 - - - +
192B ARG* 3.8 33.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 77 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B ILE* 5.0 2.5 - - + -
23B MET* 6.1 1.1 - - + -
26B HIS* 4.0 22.9 - + - -
73B ASN 2.9 17.0 + - - +
74B HIS* 3.2 5.8 + + - +
76B ILE* 1.3 77.4 - - - +
78B TRP* 1.3 86.9 + + - +
80B ASN* 3.0 22.3 + - + +
81B LEU* 3.4 33.0 - - + +
123B TRP* 3.8 21.5 - + + -
125B TRP* 5.4 0.2 - - - -
157B GLY* 3.2 27.4 - - - -
159B ASP* 3.8 14.8 - - + -
164B ALA* 5.4 0.4 - - + -
176B YOF 3.7 23.8 - - - -
180B ILE* 3.9 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 78 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B PRO* 4.4 11.0 - - + -
6B ASP 5.3 1.3 - - - -
7B LEU* 3.4 31.9 - - + -
8B PRO* 4.0 11.4 - - + +
9B YOF 2.8 27.2 + - - +
23B MET* 3.9 23.6 - - + -
26B HIS* 3.5 49.6 - + + -
27B HIS* 3.7 29.5 - + + -
31B HIS* 3.4 18.5 + - + -
74B HIS* 3.1 36.8 + + + -
75B SER* 3.7 9.4 + - - +
76B ILE 3.2 0.4 + - - -
77B PHE* 1.3 94.8 - + - +
79B THR* 1.3 61.8 + - + +
81B LEU* 3.3 11.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 79 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B PRO* 4.5 14.6 - - + -
75B SER 3.4 15.3 - - - +
76B ILE 2.7 17.6 + - - -
78B TRP* 1.3 78.7 - - + +
80B ASN* 1.3 56.4 + - - +
81B LEU 3.2 1.8 - - - -
185B ASN* 3.3 14.0 + - - -
188B ASN* 3.1 37.9 + - - +
192B ARG* 2.9 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 80 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B ILE* 3.0 24.2 + - - +
77B PHE* 3.0 13.5 + - - +
79B THR* 1.3 75.9 + - - +
81B LEU* 1.3 60.3 + - + +
155B LEU 3.2 17.5 + - - -
156B LEU* 3.4 18.2 - - + -
157B GLY* 2.9 31.8 + - - +
184B ILE* 3.5 12.1 - - - +
185B ASN* 2.7 28.5 + - - +
188B ASN* 2.9 28.7 + - - -
189B VAL* 4.3 2.8 - - - +
192B ARG* 3.7 5.7 - - - +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il