Contacts of the strand formed by residues 34 - 42 (chain A) in PDB entry 1ICN
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 ASP 34 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A VAL* 4.2 0.5 - - - +
14A TYR* 4.7 1.4 + - - -
30A LEU 3.7 3.4 - - - +
31A GLY 3.2 17.5 - - - +
32A ALA 4.0 0.2 + - - -
33A HIS* 1.3 74.8 - - - +
35A ASN* 1.3 68.0 + - - +
36A LEU* 3.1 21.5 + - - +
53A SER* 3.5 3.8 - - - -
54A ASN* 2.9 34.7 + - - +
55A PHE* 3.6 29.6 - - + -
126A ARG* 2.8 40.4 + - - -
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Residues in contact with ASN 35 (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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7A LYS* 3.0 29.1 + - - +
8A VAL* 4.4 6.7 - - - +
33A HIS* 3.4 4.7 + - - +
34A ASP* 1.3 79.2 + - - +
36A LEU* 1.3 65.8 + - - +
37A LYS* 3.3 2.9 + - - +
52A SER 3.7 5.6 - - - +
53A SER* 4.4 1.4 - - - -
54A ASN* 3.0 32.1 + - - +
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Residues in contact with LEU 36 (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 TRP 4.1 0.2 - - - +
7A LYS* 3.3 4.0 - - - +
8A VAL* 2.9 35.4 + - + +
34A ASP* 3.1 23.3 + - - +
35A ASN* 1.3 76.7 - - - +
37A LYS* 1.3 68.1 + - - +
38A LEU* 4.1 12.6 - - + -
51A GLU* 3.8 30.5 - - + +
52A SER 3.5 11.7 - - - +
53A SER* 3.9 9.6 - - - -
115A GLN* 5.4 2.5 - - - +
117A TYR* 5.6 1.3 - - - +
126A ARG* 3.7 20.6 - - - +
128A PHE* 3.8 26.9 - - + -
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Residues in contact with LYS 37 (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 THR* 3.6 28.0 - - + -
6A TRP 3.2 11.2 - - - +
7A LYS* 3.6 19.1 - - + +
35A ASN 4.2 2.5 - - - +
36A LEU* 1.3 75.5 - - - +
38A LEU* 1.3 67.8 + - - +
39A THR* 4.1 9.0 - - - +
50A LYS 3.6 1.4 - - - +
52A SER* 3.0 49.2 + - - +
131A GLU* 4.9 8.0 + - - +
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Residues in contact with LEU 38 (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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4A GLY 3.7 1.4 - - - +
5A THR* 3.3 2.9 - - - +
6A TRP* 2.8 38.9 + - + +
36A LEU* 4.1 18.8 - - + -
37A LYS* 1.3 81.6 - - - +
39A THR* 1.3 63.3 + - - +
40A ILE* 4.0 16.4 - - + -
49A VAL* 4.2 18.4 - - + -
50A LYS 3.4 2.7 - - - -
51A GLU* 4.2 13.2 - - + +
106A GLN* 4.7 2.0 - - - +
113A LEU* 4.6 11.2 - - + -
115A GLN* 3.7 25.6 - - - +
128A PHE* 4.0 25.8 - - + -
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Residues in contact with THR 39 (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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4A GLY* 3.5 5.2 - - - +
5A THR* 3.3 29.1 + - - +
37A LYS* 4.1 10.9 - - - +
38A LEU* 1.3 72.8 + - - +
40A ILE* 1.3 62.3 + - - +
41A THR* 4.8 13.9 - - + +
48A THR 3.5 2.4 - - - +
49A VAL* 3.3 4.5 - - - -
50A LYS* 2.8 54.8 + - + +
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Residues in contact with ILE 40 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A PHE* 3.5 42.2 - - + +
3A ASP* 3.6 5.5 - - - +
4A GLY 2.9 27.8 + - - +
6A TRP* 3.9 17.9 - - + +
38A LEU* 4.4 12.8 - - + -
39A THR* 1.3 78.4 - - - +
41A THR* 1.3 68.0 + - - +
42A GLN* 6.0 0.2 - - + -
47A PHE* 4.1 22.7 - - + -
48A THR 3.7 2.7 - - - -
49A VAL* 4.2 22.4 - - + -
106A GLN* 4.7 8.7 - - - +
113A LEU* 4.3 15.5 - - + -
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Residues in contact with THR 41 (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 ASP* 5.0 3.1 - - - -
39A THR* 4.8 13.9 - - + +
40A ILE* 1.3 82.9 - - - +
42A GLN* 1.3 63.6 + - - +
47A PHE* 3.5 5.0 - - - -
48A THR* 2.9 48.3 + - - +
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Residues in contact with GLN 42 (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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1A ALA* 4.8 11.3 - - - +
3A ASP* 4.3 17.6 + - - +
41A THR* 1.3 77.8 - - - +
43A GLU* 1.3 65.8 + - - +
44A GLY* 3.0 27.2 + - - +
46A LYS 3.4 7.0 - - - +
47A PHE* 3.2 39.8 - - + -
64A LEU* 5.3 2.4 - - - +
84A MET* 4.7 10.8 - - - +
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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