Contacts of the helix formed by residues 71 - 85 (chain B) in PDB entry 3IAB
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 ALA 71 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B VAL* 3.8 24.9 - - + +
36B LYS 4.1 4.5 - - - +
37B SER* 4.0 22.2 + - - +
68B MSE 3.0 13.8 + - - +
69B GLY 3.0 0.6 + - - -
70B LYS* 1.3 77.8 - - - +
72B VAL* 1.3 60.7 + - - +
73B GLU 3.4 0.9 - - - -
74B LYS* 3.3 11.7 + - - +
75B THR* 2.7 35.8 + - - +
91R A 3.8 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 72 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A ILE* 3.9 21.5 - - + -
89A GLN* 4.1 13.5 - - + +
92A LEU* 3.7 33.7 - - + -
67B GLY 4.2 2.7 - - - +
68B MSE 3.8 11.0 + - - +
69B GLY 3.0 32.5 + - - +
70B LYS 3.3 0.4 - - - -
71B ALA* 1.3 77.7 - - - +
73B GLU* 1.3 64.8 + - - +
75B THR* 3.3 6.4 + - - -
76B LEU* 3.0 31.7 + - + +
132B SER 4.0 4.3 - - - +
133B GLY* 4.2 4.9 - - - -
134B VAL* 4.6 4.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 73 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A GLY* 3.4 37.5 - - - +
86A PRO* 3.5 23.6 - - + +
88A ILE* 5.5 0.2 - - - -
89A GLN* 5.7 1.6 + - - +
135A VAL* 4.6 6.2 - - - +
136A PRO* 3.6 22.6 - - + +
70B LYS 4.5 5.2 + - - +
71B ALA 3.4 0.6 - - - -
72B VAL* 1.3 80.8 - - - +
74B LYS* 1.3 57.6 + - - +
76B LEU* 3.3 2.8 + - - -
77B ALA* 2.8 27.2 + - - +
68R A 3.5 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 74 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B VAL* 3.6 17.0 - - - -
36B LYS 2.8 29.2 + - - -
37B SER* 2.8 25.0 + - - +
39B THR* 2.9 24.6 + - + +
40B PRO 5.0 1.1 - - - +
41B TYR* 4.7 9.4 - - + +
44B ALA* 6.1 0.4 - - + -
70B LYS 5.3 0.6 + - - +
71B ALA* 3.3 11.1 + - - +
73B GLU* 1.3 75.2 - - - +
75B THR* 1.3 65.1 + - - +
77B ALA* 3.2 3.0 + - - +
78B LEU* 3.0 34.5 + - + +
68R A 3.3 58.4 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
35B VAL* 3.7 13.0 - - + +
65B VAL* 4.0 31.5 - - + +
66B LEU 4.3 0.7 - - - -
67B GLY* 3.6 29.6 - - - +
71B ALA 2.7 24.7 + - - -
72B VAL* 3.5 7.2 - - - -
74B LYS* 1.3 75.8 - - - +
76B LEU* 1.3 62.1 + - - +
78B LEU* 3.3 16.8 + - - +
79B GLY 3.3 14.6 + - - -
134B VAL* 4.8 8.1 - - + +
136B LEU* 3.7 12.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 76 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A ILE* 3.7 41.7 - - + -
115A LEU* 3.8 19.2 - - + +
136A PRO* 3.8 12.3 - - + -
138A LEU* 4.9 7.4 - - + -
72B VAL* 3.0 26.4 + - + +
73B GLU 3.7 3.6 - - - +
75B THR* 1.3 71.6 - - - +
77B ALA* 1.3 60.0 + - - +
78B LEU 3.1 2.0 - - - -
79B GLY* 3.0 3.5 + - - -
80B CYS* 2.9 33.1 + - - -
92B VAL* 4.2 9.4 - - + -
134B VAL* 3.7 35.7 - - + -
136B LEU* 3.8 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 77 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A LYS* 3.5 28.1 - - - +
136A PRO* 4.2 4.9 - - + +
41B TYR* 3.6 15.7 + - + -
73B GLU 2.8 15.4 + - - +
74B LYS* 3.2 14.1 + - - +
76B LEU* 1.3 76.2 - - - +
78B LEU* 1.3 61.6 + - - +
80B CYS* 3.4 11.8 + - - +
81B HIS 3.3 15.1 + - - -
68R A 4.2 12.8 - - - +
71R A 4.2 4.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 78 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B VAL* 4.2 14.8 - - + -
41B TYR* 3.6 45.3 - - + +
44B ALA* 3.8 24.0 - - + -
45B LEU* 3.8 17.5 - - + +
48B ILE* 4.3 17.3 - - + -
65B VAL* 5.1 2.7 - - + -
74B LYS* 3.0 27.5 + - + +
75B THR* 3.4 16.2 - - - +
76B LEU 3.1 0.2 - - - -
77B ALA* 1.3 75.5 - - - +
79B GLY* 1.3 60.4 + - - +
80B CYS 3.1 0.2 - - - -
81B HIS* 3.0 17.5 + - - +
82B PHE* 3.2 20.6 + - + -
136B LEU* 5.3 0.7 - - + -
138B ILE* 5.4 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 79 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A LEU* 4.2 1.6 - - - -
75B THR 3.3 5.1 + - - -
76B LEU 3.0 8.3 + - - -
78B LEU* 1.3 77.9 - - - +
80B CYS* 1.3 57.4 + - - +
82B PHE* 4.3 1.1 - - - +
83B GLN* 3.2 29.8 + - - +
90B ILE* 3.4 12.7 - - - +
136B LEU* 3.7 32.4 - - - +
138B ILE* 4.9 4.3 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
115A LEU* 3.7 16.2 - - - -
116A THR* 3.6 14.6 - - - -
117A SER* 3.6 23.8 - - - +
134A LYS* 3.6 23.9 - - + -
136A PRO* 3.9 10.1 - - - -
76B LEU 2.9 18.4 + - - -
77B ALA* 3.4 10.3 - - - +
78B LEU 3.1 0.2 - - - -
79B GLY* 1.3 75.9 - - - +
81B HIS* 1.3 64.7 + - - +
83B GLN* 4.5 7.2 - - - -
84B ASP* 3.2 30.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 81 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A LYS* 4.4 10.7 - - + +
41B TYR* 3.3 26.7 - + - +
45B LEU* 3.4 36.9 - - + +
77B ALA 3.3 2.2 + - - +
78B LEU 3.0 9.0 + - - +
80B CYS* 1.3 78.9 - - - +
82B PHE* 1.3 64.8 + + - +
85B GLN* 2.9 49.0 + - + +
86B LYS* 3.4 42.3 + - + -
72R U 5.0 4.8 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 82 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B LEU* 3.6 32.1 - - + -
48B ILE* 3.5 35.9 - - + -
49B ASN* 3.4 18.2 - - - -
52B LEU* 3.4 33.0 - - + -
78B LEU 3.2 23.1 + - - +
79B GLY 4.4 2.2 - - - +
81B HIS* 1.3 85.1 - + - +
83B GLN* 1.3 62.5 + - - +
86B LYS* 3.2 29.4 - - + -
88B LYS* 2.9 36.4 + - + +
90B ILE* 5.1 0.7 - - + -
138B ILE* 4.1 27.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 83 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A LYS* 4.1 14.9 - - - +
115A LEU* 3.0 30.2 + - - +
116A THR* 4.5 3.5 - - - -
154A SER 5.8 0.2 + - - -
79B GLY 3.2 19.8 + - - +
80B CYS* 4.1 4.2 - - - +
82B PHE* 1.3 76.9 - - - +
84B ASP* 1.3 70.3 + - - +
87B ASN* 3.5 18.5 + - - -
88B LYS* 3.5 20.6 + - - +
90B ILE* 3.4 35.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 84 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A THR* 5.4 2.8 + - - -
117A SER* 3.6 11.8 + - - -
132A ARG* 5.6 0.2 - - - +
134A LYS* 3.2 21.0 + - - +
80B CYS* 3.2 15.9 + - - +
83B GLN* 1.3 99.9 - - - +
85B GLN* 1.3 78.9 + - - +
86B LYS 3.2 1.3 - - - -
87B ASN* 3.3 20.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 85 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A ARG* 2.9 46.3 + - - +
134A LYS* 3.2 39.6 - - - +
81B HIS* 2.9 35.1 + - + +
84B ASP* 1.3 84.3 - - - +
86B LYS* 1.3 63.9 + - + +
87B ASN* 3.7 3.1 - - - +
----------------------------------------------------------
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