Contacts of the strand formed by residues 70 - 83 (chain B) in PDB entry 4ICK
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 LEU 70 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B LEU* 3.5 28.9 - - + -
10B ILE* 3.7 20.2 - - + -
56B LEU* 4.1 16.8 - - + +
59B THR* 4.0 15.7 - - + -
65B ILE* 3.7 20.9 - - + +
66B GLU 3.6 17.3 - - - +
67B ALA* 3.1 13.5 + - - +
68B GLY 3.3 1.0 - - - -
69B GLN* 1.3 80.3 - - - +
71B THR* 1.3 60.8 + - - +
72B ILE* 4.2 1.5 + - + +
96B ALA* 4.2 7.6 - - + -
97B GLU 3.5 11.4 - - - +
98B VAL* 4.1 7.6 - - + -
99B LYS* 2.7 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 71 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B LEU* 1.3 77.4 + - - +
72B ILE* 1.3 72.5 + - - +
73B ILE* 3.5 11.0 + - + +
96B ALA* 3.2 4.8 - - - -
97B GLU* 2.9 40.6 + - - +
99B LYS* 3.6 18.0 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
8B LEU* 3.7 29.4 - - + -
52B LEU* 4.0 28.7 - - + -
56B LEU* 4.0 24.9 - - + -
70B LEU* 4.2 3.0 + - + -
71B THR* 1.3 78.9 - - - +
73B ILE* 1.3 72.2 + - - +
74B GLU* 3.4 5.6 + - - +
94B TRP* 4.6 14.4 - - + -
95B LEU 3.7 6.3 - - - +
96B ALA* 4.2 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 73 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B PHE* 3.8 35.7 - - + -
13B ARG* 5.7 1.1 - - - +
71B THR* 3.9 20.0 - - + +
72B ILE* 1.3 77.7 - - - +
74B GLU* 1.3 62.4 + - - +
75B GLY 3.6 1.7 + - - -
76B PHE* 3.9 14.2 + - - +
94B TRP* 5.6 0.3 - - - -
95B LEU* 2.9 31.6 + - + +
97B GLU* 4.3 11.9 - - + +
141B PHE* 3.4 30.7 - - + -
142B LEU* 4.3 4.9 - - + -
145B ILE* 3.9 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 74 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A GLN* 5.6 2.7 - - + +
143A CYS 4.9 0.5 - - - +
144A SER* 3.7 27.7 - - - +
147A ALA* 4.0 16.1 - - - +
72B ILE* 3.4 8.5 + - - +
73B ILE* 1.3 73.2 - - - +
75B GLY* 1.3 61.2 + - - +
141B PHE* 3.3 19.4 - - - -
145B ILE* 5.0 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 75 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A GLU 4.6 1.9 - - - +
140A GLN* 3.9 31.3 - - - +
141A PHE* 3.6 23.2 + - - +
144A SER* 3.5 20.4 - - - -
73B ILE 3.6 0.2 + - - -
74B GLU* 1.3 77.3 - - - +
76B PHE* 1.3 60.2 + - - +
78B ARG* 5.2 1.4 + - - -
141B PHE* 3.7 11.1 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
140A GLN* 4.3 4.1 + - - +
9B ILE* 4.3 15.0 - - + -
73B ILE 3.9 9.3 + - - +
74B GLU 3.5 1.6 - - - -
75B GLY* 1.3 81.3 + - - +
77B LYS* 1.3 65.4 + - - +
78B ARG* 3.4 57.0 - - + +
93B TYR 4.7 2.5 - - - -
94B TRP* 3.6 19.9 - - - -
95B LEU* 3.7 31.5 + - + -
134B ALA 3.8 5.2 - - - -
137B GLU 3.6 5.6 - - - -
138B GLY* 3.5 32.8 - - - -
141B PHE* 3.6 37.9 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 77 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A GLN* 6.0 4.0 - - - -
137A GLU* 3.1 27.1 - - + +
140A GLN* 3.9 17.7 + - - +
76B PHE* 1.3 79.3 - - - +
78B ARG* 1.3 85.9 + - - +
79B GLU* 6.1 1.1 - - + -
92B ILE* 3.8 18.4 - - + +
93B TYR 3.3 14.8 - - - +
94B TRP* 3.5 36.6 - - + +
202B MG 3.3 16.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 78 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A GLY 5.2 1.4 + - - -
76A PHE* 3.7 35.1 - - - +
77A LYS 2.8 26.0 + - - +
78A ARG* 3.6 12.4 - - - +
137A GLU* 3.4 19.4 + - - +
75B GLY 5.2 1.4 + - - -
76B PHE* 3.4 55.0 - - + +
77B LYS* 1.3 92.9 + - - +
79B GLU* 1.3 59.8 + - - +
80B LEU* 4.1 5.8 + - + +
91B VAL 3.7 0.9 - - - +
92B ILE* 3.5 1.3 - - - +
93B TYR* 2.8 41.0 + - + +
134B ALA* 4.3 20.0 - - + -
137B GLU* 2.9 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 79 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A ARG* 3.5 24.6 + - - +
129A LYS* 4.7 9.4 - - - +
133A ALA* 4.5 15.3 - - + +
137A GLU* 3.3 15.0 + - - +
4B ARG* 4.4 8.5 + - - -
77B LYS* 6.1 0.7 - - + -
78B ARG* 1.3 73.8 - - - +
80B LEU* 1.3 69.5 + - - +
81B ASN* 2.8 35.0 + - - +
90B THR* 3.3 11.3 + - + +
91B VAL 3.4 3.4 - - - -
92B ILE* 3.0 30.6 - - + +
130B GLU* 4.4 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 80 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B ARG* 4.2 7.0 - - + +
79B GLU* 1.3 78.6 - - - +
81B ASN* 1.3 61.5 + - - +
82B TYR* 4.2 21.9 - - + -
89B LYS 4.4 0.2 - - - -
90B THR* 3.2 6.4 - - - -
91B VAL* 2.7 40.6 + - + +
93B TYR* 3.8 29.6 - - + -
130B GLU* 3.4 23.3 - - + +
131B MET* 4.0 40.4 - - + +
134B ALA* 4.1 19.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 81 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A ARG* 4.9 1.4 + - - -
81A ASN 4.1 6.1 - - - +
129A LYS* 3.9 24.8 - - - +
130A GLU* 3.8 34.6 + - - +
79B GLU* 2.8 41.6 + - - +
80B LEU* 1.3 72.7 + - - +
82B TYR* 1.3 62.8 + - - +
89B LYS 3.4 3.8 - - - +
90B THR* 3.1 20.8 + - - -
130B GLU* 2.9 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 82 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B LYS* 5.4 6.8 + - - -
80B LEU* 4.3 31.0 - - + -
81B ASN* 1.3 79.0 - - - +
83B VAL* 1.3 61.9 + - - +
84B ALA* 3.4 31.2 - - + -
88B PRO* 3.6 0.9 - - - +
89B LYS* 2.7 69.2 + - + +
91B VAL* 4.2 16.7 - - + +
130B GLU* 4.8 13.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 83 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B TYR* 1.3 79.2 - - - +
84B ALA* 1.3 60.0 + - - +
85B ARG 4.4 0.3 + - - -
86B ASN* 3.4 49.2 + - - +
87B LYS 3.5 6.5 - - - +
88B PRO* 4.2 14.8 - - + -
----------------------------------------------------------
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