Contacts of the helix formed by residues 61 - 81 (chain B) in PDB entry 2W7W
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 THR 61 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B PHE* 5.2 0.8 - - - -
60B SER* 1.3 78.8 - - - +
62B GLY* 1.3 69.9 + - - +
63B GLY 3.5 1.2 + - - -
64B VAL* 3.5 8.1 + - - +
65B PHE* 3.3 16.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 62 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B THR* 1.3 76.3 - - - +
63B GLY* 1.3 59.5 + - - -
65B PHE* 3.2 4.0 + - - +
66B ASN* 2.9 38.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 63 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B LEU* 3.5 14.7 - - - +
61B THR 3.5 0.4 + - - -
62B GLY* 1.3 69.5 - - - -
64B VAL* 1.3 65.0 + - - +
66B ASN* 4.3 8.7 - - - -
67B ASN* 2.8 31.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 64 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B LEU* 3.8 11.0 - - + +
42B LEU* 3.7 32.2 - - + +
43B ILE* 4.7 3.8 - - + -
46B THR* 6.0 1.6 - - + -
48B PHE* 3.8 26.9 - - + -
56B ILE* 3.6 19.1 - - + -
60B SER* 3.5 22.7 - - - -
61B THR 3.5 7.8 + - - +
62B GLY 3.4 0.8 - - - -
63B GLY* 1.3 74.7 - - - +
65B PHE* 1.3 63.4 + - - +
68B ALA* 3.0 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 65 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B ILE* 3.4 35.2 - - + -
60B SER* 3.3 23.2 + - - +
61B THR* 3.3 18.3 + - - -
62B GLY 3.2 9.1 + - - +
64B VAL* 1.3 76.6 - - - +
66B ASN* 1.3 78.6 + - - +
67B ASN 3.1 0.2 + - - -
68B ALA* 3.2 2.5 + - - -
69B ALA* 2.7 47.1 + - + +
142B ALA* 4.0 16.8 - - + -
143B ALA* 4.1 16.8 - - + -
144B THR* 4.4 6.5 - - + -
147B THR* 3.9 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 66 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A PHE* 3.6 48.9 - - + +
62B GLY* 2.9 25.0 + - - +
63B GLY* 3.9 8.4 - - - +
64B VAL 3.4 0.4 - - - -
65B PHE* 1.3 86.7 - - - +
67B ASN* 1.3 64.0 + - - +
70B GLN* 3.2 29.0 + - - +
141B ASN* 5.8 0.3 - - - +
142B ALA* 3.5 17.0 + - - +
----------------------------------------------------------
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 PHE* 5.4 2.8 - - - -
35B TYR* 3.3 39.6 - - - +
38B LYS* 3.4 40.2 - - - +
39B LEU* 4.0 12.3 - - + +
42B LEU* 3.9 6.4 - - - +
63B GLY* 2.8 26.5 + - - +
64B VAL 4.2 1.1 - - - +
66B ASN* 1.3 79.5 - - - +
68B ALA* 1.3 66.1 + - - +
70B GLN* 3.4 2.6 + - - +
71B ILE* 3.1 28.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 68 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B LEU* 3.7 22.8 - - + +
53B LEU* 3.8 7.3 - - + +
56B ILE* 3.7 25.8 - - + -
57B ILE* 3.5 21.8 - - + +
64B VAL 3.0 18.1 + - - +
65B PHE 4.0 1.6 - - - +
67B ASN* 1.3 75.8 - - - +
69B ALA* 1.3 63.3 + - - +
71B ILE* 3.1 13.5 + - - +
72B TRP 3.3 9.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 69 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B ILE* 3.7 13.6 - - + +
65B PHE* 2.7 43.8 + - + +
68B ALA* 1.3 73.8 - - - +
70B GLN* 1.3 57.2 + - - +
72B TRP* 3.3 3.7 + - - +
73B ASN* 2.8 34.9 + - - +
142B ALA* 3.4 22.9 - - + +
144B THR* 4.1 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 70 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A PHE* 4.2 3.8 - - + -
35B TYR* 3.1 53.2 + - + -
66B ASN 3.2 19.8 + - - +
67B ASN 3.8 0.2 - - - +
68B ALA 3.3 0.2 - - - -
69B ALA* 1.3 73.8 - - - +
71B ILE* 1.3 66.5 + - - +
73B ASN* 3.1 26.8 + - - -
74B HIS* 2.7 44.2 + - - -
123B TRP* 3.1 14.3 + - - -
141B ASN 4.1 0.4 - - - -
142B ALA* 3.5 17.5 - - + -
160B TRP* 3.4 25.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 71 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B PHE* 5.0 7.9 - - + -
4B GLU 5.4 1.8 - - - +
6B PRO* 4.8 7.6 - - + -
32B HIS* 3.0 26.0 + - + +
35B TYR* 3.7 18.4 - - + +
36B VAL* 3.7 36.6 - - + +
39B LEU* 3.6 31.9 - - + -
53B LEU* 4.0 18.6 - - + -
67B ASN 3.1 15.8 + - - +
68B ALA 3.1 5.6 + - - +
70B GLN* 1.3 76.0 - - - +
72B TRP* 1.3 61.7 - - - +
75B THR* 3.0 26.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 72 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B LEU* 4.0 14.5 - - + +
54B GLU* 2.9 41.3 + - + -
57B ILE* 3.5 22.4 - - + -
68B ALA 3.3 2.2 + - - +
69B ALA 3.3 3.9 + - - +
71B ILE* 1.3 74.8 - - - +
73B ASN* 1.3 68.9 + - - +
75B THR* 3.1 8.1 + - - -
76B PHE* 2.9 73.9 + + + +
125B TRP* 4.0 17.5 - + - -
144B THR* 4.0 11.7 - - + -
146B LEU* 3.7 27.8 - - + -
153B PRO* 3.7 21.3 - - + -
----------------------------------------------------------
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 ALA 2.8 24.9 + - - +
70B GLN* 3.1 19.1 + - - +
72B TRP* 1.3 78.6 - - - +
74B HIS* 1.3 59.1 + - - +
76B PHE* 3.6 3.2 + - - +
77B TYR* 2.9 27.9 + - - +
123B TRP* 3.4 33.9 - - + +
125B TRP* 3.3 24.2 - - - -
142B ALA 3.0 27.7 + - - -
143B ALA 3.9 3.6 + - - -
144B THR* 3.4 13.6 + - - -
156B THR* 4.6 0.7 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
27B HIS* 3.1 21.1 + + - -
31B HIS* 5.2 0.2 - - - +
32B HIS* 3.5 32.8 - + + +
35B TYR* 3.5 28.1 - + - -
70B GLN* 2.7 41.6 + - - +
73B ASN* 1.3 73.9 - - - +
75B THR* 1.3 67.8 + - - +
77B TYR* 3.1 6.7 + + - +
78B TRP* 2.9 39.7 + + - +
123B TRP* 3.7 10.9 - + - -
158B ASP* 3.3 3.9 + - - -
162B HIS* 3.8 0.4 + - - -
1195B FE 2.2 31.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 75 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B PRO* 3.3 35.5 - - + +
32B HIS* 3.3 6.5 - - - -
71B ILE* 3.0 17.5 + - - +
72B TRP* 3.1 10.7 + - - -
74B HIS* 1.3 75.7 - - - +
76B PHE* 1.3 63.5 + - - +
78B TRP* 3.4 7.3 + - - +
79B ASN* 3.2 32.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 76 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B TRP* 2.9 51.5 + + + +
73B ASN 3.7 3.6 - - - +
75B THR* 1.3 77.9 - - - +
77B TYR* 1.3 62.0 + - - +
79B ASN* 3.1 11.6 + - - +
80B CYS* 3.1 38.9 + - - -
125B TRP* 4.0 12.1 - + - -
153B PRO* 3.5 33.2 - - + -
154B LEU 3.7 2.7 - - - -
155B LEU 3.8 4.5 - - - -
156B THR* 3.7 27.4 - - + -
187B PHE* 3.8 12.3 - + - -
191B ASN* 3.6 25.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 77 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B ILE* 4.0 12.8 - - - +
27B HIS* 3.6 26.5 + + - -
73B ASN 2.9 18.7 + - - +
74B HIS* 3.1 8.0 + + - +
76B PHE* 1.3 75.1 - - - +
78B TRP* 1.3 84.0 + + - +
80B CYS* 2.8 24.9 + - - +
81B LEU* 3.5 25.0 + - + +
123B TRP* 3.9 8.5 - - + -
156B THR* 3.8 20.2 - - + -
157B VAL* 4.2 7.4 - - + -
158B ASP* 3.5 34.8 - - + -
163B ALA* 4.5 4.3 + - - +
175B TYR* 2.7 30.5 + - - -
179B PHE* 4.9 1.6 - + - -
----------------------------------------------------------
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
----------------------------------------------------------
6B PRO* 5.6 2.2 - - + -
7B ALA 5.6 1.1 - - - -
8B LEU* 3.5 23.3 - - + -
9B PRO* 3.6 22.9 - - + +
10B PHE* 3.2 14.0 - + + -
19B ILE* 6.5 0.2 - - + -
23B THR* 6.4 0.2 - - + -
24B LEU* 3.8 23.3 - - + -
27B HIS* 3.5 39.9 - + + -
28B HIS* 3.7 31.4 - + + -
32B HIS* 3.0 27.6 + + - -
74B HIS* 2.9 39.4 + + + -
75B THR* 3.9 7.0 - - + +
77B TYR* 1.3 97.9 - + - +
79B ASN* 1.3 63.2 + - - +
81B LEU* 3.1 30.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 79 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B PRO* 3.8 23.5 - - - +
75B THR* 3.2 23.7 + - - +
76B PHE* 3.1 10.8 + - - +
78B TRP* 1.3 77.8 - - - +
80B CYS* 1.3 57.1 + - - +
81B LEU 3.3 1.1 - - - -
184B ASN* 3.0 27.1 + - - +
187B PHE* 3.2 41.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 80 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B PHE* 3.1 33.5 + - - -
77B TYR* 2.8 11.9 + - - +
79B ASN* 1.3 77.1 - - - +
81B LEU* 1.3 61.6 + - + +
154B LEU 4.7 0.2 - - - -
155B LEU* 3.9 18.6 - - + -
156B THR 3.6 35.0 - - - +
179B PHE* 5.1 0.4 - - + -
183B VAL* 3.3 9.7 - - - +
184B ASN* 2.6 30.7 + - - -
187B PHE* 3.8 12.3 - - - -
188B VAL* 5.5 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 81 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B PRO* 5.2 0.5 - - - +
10B PHE* 3.4 18.2 - - + -
15B LEU* 4.2 22.4 - - + -
19B ILE* 4.4 8.5 - - + -
24B LEU* 5.9 0.2 - - + -
77B TYR* 3.7 44.4 - - + +
78B TRP* 3.1 29.2 + - + +
79B ASN* 4.0 2.4 - - - +
80B CYS* 1.3 86.9 - - + +
82B ALA* 1.3 65.8 + - - +
179B PHE* 4.1 27.8 - - + -
182B LEU* 3.3 26.0 - - + +
184B ASN* 4.0 4.6 + - - +
----------------------------------------------------------
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