Contacts of the strand formed by residues 3 - 12 (chain A) in PDB entry 1I1B
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 VAL 3 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A ARG* 1.3 67.7 - - - +
5A SER* 4.0 3.7 + - - +
45A SER* 4.3 9.4 - - - +
46A PHE 3.2 30.5 - - - +
47A VAL* 4.5 0.4 - - + -
91A PRO* 3.7 40.2 - - + +
92A LYS* 3.9 10.3 - - - +
93A LYS* 3.8 33.2 - - + +
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Residues in contact with ARG 4 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A VAL* 1.3 76.9 - - - +
5A SER* 1.3 62.2 - - - +
45A SER* 3.4 2.9 - - - -
46A PHE* 2.9 50.2 + - + +
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Residues in contact with SER 5 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A VAL* 4.0 5.0 + - - +
4A ARG* 1.3 74.5 - - - +
6A LEU* 1.3 69.1 - - - +
7A ASN* 5.8 0.2 - - - -
43A SER* 3.6 19.0 + - - -
44A MET 3.2 8.5 - - - -
45A SER* 2.9 22.7 + - - -
46A PHE* 4.7 3.1 - - - -
91A PRO* 4.6 7.4 - - - +
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Residues in contact with LEU 6 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A SER* 1.3 82.6 - - - +
7A ASN* 1.3 66.2 + - - +
43A SER* 3.6 1.3 - - - -
44A MET* 2.8 38.4 + - + +
46A PHE* 3.8 28.5 - - + -
148A MET* 3.4 31.0 - - + -
150A PHE* 3.8 26.7 - - + -
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Residues in contact with ASN 7 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A SER* 5.8 0.2 - - - -
6A LEU* 1.3 78.4 - - - +
8A CYS* 1.3 67.4 + - - +
41A VAL* 3.9 4.3 - - + -
42A PHE 3.2 10.6 - - - +
43A SER* 3.9 11.1 + - - -
63A LYS* 3.7 29.6 - - + +
150A PHE* 3.8 5.4 - - - +
151A VAL* 3.4 40.9 + - + +
152A SER 3.8 18.4 + - - +
153A SER* 4.1 17.8 + - - +
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Residues in contact with CYS 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A LEU 4.5 0.2 - - - -
7A ASN* 1.3 80.1 - - - +
9A THR* 1.3 68.2 + - - +
10A LEU* 5.1 3.4 - - - -
41A VAL* 3.6 3.0 - - - +
42A PHE* 2.9 47.2 + - - +
44A MET* 4.2 26.2 - - - -
60A LEU* 5.6 0.2 - - - -
148A MET* 3.5 33.9 - - + -
149A GLN 3.0 15.5 - - - +
151A VAL* 3.8 5.9 - - - +
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Residues in contact with THR 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A CYS* 1.3 80.6 - - - +
10A LEU* 1.3 62.7 + - - +
11A ARG* 4.9 0.9 + - - -
39A GLN* 3.8 37.9 + - - +
40A VAL 3.8 16.4 - - - +
41A VAL* 3.9 18.4 - - + -
42A PHE* 4.7 0.7 - - - -
148A MET* 3.4 6.8 - - - +
149A GLN* 2.8 57.5 + - - +
151A VAL* 4.1 13.1 - - + +
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Residues in contact with LEU 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A CYS* 5.1 3.4 - - - -
9A THR* 1.3 78.7 - - - +
11A ARG* 1.3 64.8 - - - +
17A SER* 4.5 1.9 - - - -
18A LEU* 4.1 33.3 + - + +
39A GLN* 4.6 6.1 - - - +
40A VAL 5.1 0.6 + - - -
42A PHE* 4.1 30.3 - - + -
44A MET* 5.1 2.9 - - + -
60A LEU* 4.9 13.7 - - + -
69A LEU* 6.4 0.2 - - + -
110A LEU* 4.7 0.4 - - + -
112A PHE* 3.9 39.9 - - + -
122A ILE* 5.9 3.4 - - + -
146A PHE* 4.2 18.2 - - + -
147A THR 3.2 12.6 - - - +
148A MET* 4.1 16.8 - - + -
149A GLN* 4.0 1.6 - - - +
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Residues in contact with ARG 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A THR* 4.9 0.8 + - - -
10A LEU* 1.3 76.6 - - - +
12A ASP* 1.3 63.7 + - - +
15A GLN* 3.4 43.0 + - - +
16A LYS 3.1 20.2 - - - +
17A SER* 3.8 12.6 + - - +
18A LEU* 5.6 0.2 - - - -
36A MET* 4.8 14.3 - - - +
39A GLN* 4.4 14.1 + - - +
146A PHE* 3.1 6.3 - - - -
147A THR* 2.8 34.3 + - - +
149A GLN* 3.9 41.6 + - - +
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Residues in contact with ASP 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A ARG* 1.3 78.5 - - - +
13A SER* 1.3 60.0 + - - +
14A GLN* 2.8 38.4 + - - +
15A GLN* 2.9 13.9 + - - +
16A LYS* 2.9 55.3 + - - +
18A LEU* 5.5 1.0 - - + +
28A ALA* 5.4 0.2 - - - -
124A THR* 2.7 27.2 + - + +
143A ILE* 3.6 16.5 - - + +
145A ASP 3.4 5.6 - - - -
146A PHE* 3.7 19.0 - - + -
147A THR* 5.2 1.7 + - - +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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