Contacts of the helix formed by residues 61 - 78 (chain B) in PDB entry 1ISA
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 GLY 61 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B GLU* 1.3 80.0 + - - +
62B GLY* 1.3 58.1 + - - -
64B PHE* 3.6 2.7 - - - +
65B ASN* 2.9 39.9 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
41B LEU* 3.6 15.0 - - - +
60B GLU 3.4 0.8 + - - -
61B GLY* 1.3 69.4 - - - -
63B VAL* 1.3 64.2 + - - +
65B ASN* 3.3 8.2 + - - +
66B ASN* 2.9 31.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 63 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B LEU* 3.9 5.9 - - + +
41B LEU* 4.0 30.4 - - + +
42B ILE* 4.2 12.6 - - + -
47B PHE* 4.1 27.4 - - + -
55B ILE* 3.8 17.3 - - + -
59B SER* 3.7 18.8 - - - -
60B GLU 3.6 7.6 + - - +
61B GLY 3.4 0.2 - - - -
62B GLY* 1.3 74.0 - - - +
64B PHE* 1.3 64.8 + - - +
67B ALA* 3.0 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 64 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B ILE* 3.3 37.9 - - + -
59B SER* 3.3 24.5 + - - +
60B GLU* 3.3 17.9 + - - -
61B GLY 3.3 9.3 + - - +
63B VAL* 1.3 79.5 - - - +
65B ASN* 1.3 69.4 + - - +
67B ALA* 3.3 2.4 + - - -
68B ALA* 2.8 43.1 + - + +
141B ALA* 4.0 24.7 - - + -
142B GLY* 4.6 7.2 - - - -
143B THR* 4.3 4.9 - - + -
146B THR* 3.8 23.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 65 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A PHE* 3.6 49.7 - - + +
61B GLY* 2.9 26.5 + - - +
62B GLY* 3.8 7.8 - - - +
63B VAL 3.3 0.4 - - - -
64B PHE* 1.3 90.0 - - - +
66B ASN* 1.3 64.6 + - - +
69B GLN* 3.1 31.3 + - - +
140B ASN* 5.7 0.7 - - - +
141B ALA* 3.6 9.0 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
118A PHE* 5.3 3.6 - - - -
34B TYR* 3.4 37.8 - - - +
37B ASN* 3.4 32.3 + - - +
38B LEU* 4.0 13.2 - - + +
41B LEU* 3.6 13.1 - - + +
62B GLY* 2.9 23.3 + - - +
63B VAL 4.2 0.9 - - - +
65B ASN* 1.3 78.8 - - - +
67B ALA* 1.3 59.2 + - - +
69B GLN* 3.2 5.4 + - - +
70B VAL* 2.9 34.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 67 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B LEU* 3.7 19.2 - - + +
52B LEU* 3.8 8.8 - - + +
55B ILE* 3.7 25.6 - - + -
56B ILE* 3.7 19.5 - - + +
63B VAL 3.0 20.6 + - - +
64B PHE* 3.8 2.7 - - - +
66B ASN* 1.3 77.0 - - - +
68B ALA* 1.3 61.7 + - - +
70B VAL* 3.3 4.2 + - - +
71B TRP 3.2 17.7 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
56B ILE* 3.8 13.1 - - + +
64B PHE* 2.8 38.1 + - + +
67B ALA* 1.3 71.3 - - - +
69B GLN* 1.3 56.8 + - - +
71B TRP* 3.2 2.1 + - - +
72B ASN* 2.8 35.2 + - - +
141B ALA* 3.3 27.8 - - + +
143B THR* 4.1 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 69 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A PHE* 4.0 3.8 - - + -
31B HIS* 4.4 0.2 - - - -
34B TYR* 3.1 52.2 + - + -
65B ASN 3.1 21.3 + - - +
66B ASN 3.2 1.1 + - - +
68B ALA* 1.3 75.7 - - - +
70B VAL* 1.3 61.2 + - - +
72B ASN* 3.3 6.4 + - - +
73B HIS* 2.7 45.3 + - - -
122B TRP* 3.1 27.8 + - - -
141B ALA* 3.6 16.4 - - + -
158B TRP* 3.3 25.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 70 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B PHE* 5.6 4.9 - - + -
3B GLU 5.4 4.3 - - - +
5B PRO* 5.5 2.7 - - + -
31B HIS* 3.0 28.8 + - - +
34B TYR* 3.7 7.0 - - + +
35B VAL* 3.7 47.6 - - + +
38B LEU* 4.2 11.7 - - + -
52B LEU* 4.1 21.1 - - + -
66B ASN 2.9 18.6 + - - +
67B ALA 3.6 7.6 - - - +
69B GLN* 1.3 75.0 - - - +
71B TRP* 1.3 64.0 + - - +
74B THR* 3.1 17.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 71 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B LEU* 4.0 19.3 - - + +
53B GLU* 3.3 28.0 + - - +
56B ILE* 3.6 26.0 - - + -
67B ALA 3.2 3.3 + - - +
68B ALA 3.7 2.5 - - - +
70B VAL* 1.3 78.5 - - - +
72B ASN* 1.3 80.8 + - - +
74B THR* 3.2 6.9 + - - -
75B PHE* 3.0 58.2 + + + -
124B TRP* 4.1 10.3 - + - -
143B THR* 4.1 15.7 - - - -
145B LEU* 3.7 28.6 - - + +
151B PRO* 3.9 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 72 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B ALA* 2.8 25.5 + - - +
69B GLN* 3.3 15.1 + - - +
71B TRP* 1.3 79.7 - - - +
73B HIS* 1.3 57.7 + - - +
75B PHE* 3.5 4.0 + - - +
76B TYR* 3.0 27.7 + - - +
122B TRP* 3.4 33.2 - - + +
124B TRP* 3.3 15.4 - - + -
141B ALA 3.3 25.1 + - - -
142B GLY 3.8 4.8 + - - -
143B THR* 3.3 23.4 + - - -
154B THR* 4.4 1.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 73 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B HIS* 3.1 21.7 + + - -
30B HIS* 5.2 0.2 - - - +
31B HIS* 3.6 29.6 - + + +
34B TYR* 3.4 29.0 - + - -
69B GLN* 2.7 45.5 + - - +
72B ASN* 1.3 74.1 - - - +
74B THR* 1.3 65.0 + - - +
76B TYR* 3.2 7.6 + + - +
77B TRP* 3.0 33.7 + + - +
122B TRP* 3.7 11.3 - + - -
156B ASP* 3.3 4.2 + - - -
160B HIS* 3.7 1.4 + - - -
193B FE2 2.0 31.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 74 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B PRO* 3.6 32.0 - - + +
31B HIS* 3.1 22.3 + - - -
70B VAL* 3.1 16.7 + - - +
71B TRP* 3.2 6.7 + - - -
73B HIS* 1.3 75.7 - - - +
75B PHE* 1.3 64.5 + - - +
77B TRP* 3.3 7.2 + - - +
78B ASN* 3.1 35.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 75 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B TRP* 3.0 49.7 + + + +
72B ASN* 3.6 4.7 - - - +
74B THR* 1.3 76.3 - - - +
76B TYR* 1.3 60.6 + - - +
78B ASN* 3.1 17.3 + - - +
79B CYS* 3.1 30.7 + - - -
124B TRP* 4.0 13.9 - + - -
151B PRO* 3.5 29.2 - - + -
152B LEU 3.6 12.1 - - - -
153B LEU 3.8 16.8 - - - -
154B THR* 3.8 16.8 - - + -
185B PHE* 3.7 22.6 - + - -
189B ASN* 3.7 13.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 76 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B ILE* 3.8 18.0 - - - +
26B HIS* 3.7 25.9 + + - -
72B ASN 3.0 18.2 + - - +
73B HIS* 3.4 7.4 - + - +
75B PHE* 1.3 76.1 - - - +
77B TRP* 1.3 92.8 + + - +
79B CYS* 3.1 14.4 + - - +
80B LEU* 3.5 30.9 - - + +
122B TRP* 3.9 11.2 - + + -
154B THR* 3.9 22.0 - - + -
155B VAL* 4.2 6.1 - - + -
156B ASP* 3.5 31.4 - - + -
161B ALA* 4.4 5.0 + - - +
173B TYR* 2.8 24.2 + - - -
177B PHE* 4.9 2.1 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 77 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B LEU* 3.7 22.9 - - + -
8B PRO* 4.2 9.6 - - + -
9B TYR* 2.7 35.4 + - - +
18B ILE* 5.5 2.5 - - + -
22B THR* 5.8 0.4 - - + -
23B ILE* 3.5 28.5 - - + -
26B HIS* 3.5 39.5 - + + -
27B TYR* 3.7 34.1 - + + -
31B HIS* 3.2 29.4 + + - -
73B HIS* 3.0 27.1 + + + +
74B THR* 3.3 7.4 + - - +
76B TYR* 1.3 95.6 - + - +
78B ASN* 1.3 61.1 + - - +
80B LEU* 3.3 20.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 78 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B PRO* 3.6 25.1 - - - +
74B THR* 3.1 27.3 + - - +
75B PHE* 3.1 10.2 + - - +
77B TRP* 1.3 73.8 - - - +
79B CYS* 1.3 59.2 + - - +
80B LEU 3.2 3.7 - - - +
182B ASN* 3.1 24.1 - - - +
185B PHE* 3.4 38.7 - - + +
----------------------------------------------------------
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