Contacts of the strand formed by residues 5 - 13 (chain A) in PDB entry 3ZS4
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 ILE 5 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A MET* 6.4 2.2 - - + -
3A PRO 4.2 7.0 - - - +
4A LEU* 1.3 74.8 - - - +
6A LEU* 1.3 70.3 + - - +
7A LEU* 4.0 10.0 - - + +
47A GLU* 4.8 21.1 - - - +
48A TRP* 3.6 36.6 - - + +
198A ILE* 5.9 1.3 - - + -
221A GLU* 3.0 41.8 + - + +
222A GLY* 3.1 5.0 - - - -
223A ALA 2.8 26.7 + - - -
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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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4A LEU* 3.7 12.3 + - + +
5A ILE* 1.3 89.2 - - - +
7A LEU* 1.3 62.4 + - - +
8A PRO* 3.5 8.9 - - + +
46A ALA* 5.3 0.7 - - - -
47A GLU* 4.6 7.1 + - - +
48A TRP* 4.1 10.9 + - - +
209A LEU* 4.0 26.2 - - + -
223A ALA 3.5 6.5 - - - +
225A VAL* 4.8 6.3 - - + -
236A LEU* 4.3 13.2 - - + -
239A ALA* 3.5 46.4 - - + +
240A LEU* 3.8 25.9 - - + +
243A VAL* 4.1 14.6 - - + -
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Residues in contact with LEU 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 ILE* 4.0 18.6 - - + +
6A LEU* 1.3 75.6 - - - +
8A PRO* 1.3 68.5 - - - +
9A ALA 3.3 0.5 + - - -
48A TRP* 3.6 35.9 - - + -
50A HIS* 4.2 13.0 - - + +
79A GLU* 3.4 26.9 - - + +
100A ARG* 4.0 14.4 - - - +
198A ILE* 4.0 18.8 - - + -
222A GLY* 4.4 2.7 - - - -
223A ALA 2.9 25.7 + - - +
224A ILE* 3.2 14.7 - - + +
225A VAL* 3.1 20.5 + - - +
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Residues in contact with PRO 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* 3.5 7.6 - - + +
7A LEU* 1.3 84.2 - - - +
9A ALA* 1.3 61.5 + - - +
41A TRP* 3.7 28.9 - - + +
46A ALA* 3.9 19.7 - - + -
48A TRP 3.3 16.2 - - - +
49A ILE* 3.6 9.5 - - + +
50A HIS 3.0 21.1 + - - -
225A VAL* 3.4 9.4 - - + +
229A LEU* 3.8 20.9 - - + -
236A LEU* 4.0 19.1 - - + -
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Residues in contact with ALA 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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7A LEU 3.3 0.6 + - - -
8A PRO* 1.3 74.1 - - - +
10A VAL* 1.3 56.0 + - - +
11A ASP* 3.7 8.3 - - - +
19A ARG* 3.7 9.2 - - - +
41A TRP* 4.1 1.2 + - - -
50A HIS* 3.3 8.1 - - - +
224A ILE* 3.7 13.5 - - + -
225A VAL 2.9 14.6 + - - +
226A GLY* 4.2 0.2 - - - -
230A TYR* 2.6 36.6 + - - -
1246A 1PR 3.4 29.2 - - - +
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Residues in contact with VAL 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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9A ALA* 1.3 73.2 - - - +
11A ASP* 1.3 61.4 + - - +
12A VAL* 4.0 10.8 - - + -
17A ALA* 4.2 8.7 - - + -
34A ALA* 3.8 24.7 - - + +
37A ALA* 4.2 0.4 - - + -
38A ALA* 4.0 13.5 - - + +
41A TRP* 4.0 14.8 - - + -
49A ILE* 3.9 18.2 - - + -
50A HIS 2.8 9.4 + - - +
51A LEU* 3.4 24.5 - - + +
52A VAL 2.9 25.1 + - - +
230A TYR* 3.3 20.0 - - - +
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Residues in contact with ASP 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 ALA* 3.7 2.8 - - - +
10A VAL* 1.3 76.2 - - - +
12A VAL* 1.3 61.6 + - - +
16A ARG 3.3 1.4 - - - +
17A ALA* 3.4 2.8 - - - +
18A VAL* 2.9 45.8 + - - +
19A ARG* 2.9 23.7 + - - +
52A VAL* 3.6 11.2 - - - +
54A LEU* 3.8 20.5 - - + +
230A TYR* 5.7 0.2 - - - -
1246A 1PR 2.4 53.0 + - - +
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Residues in contact with VAL 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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10A VAL* 3.9 3.4 - - + +
11A ASP* 1.3 75.7 - - - +
13A VAL* 1.3 63.3 + - - +
15A GLY* 3.8 22.2 - - - +
16A ARG 3.3 5.4 - - - +
34A ALA* 3.7 23.8 - - + -
51A LEU* 3.9 14.1 - - + -
52A VAL 2.8 20.4 + - - +
53A ASP* 4.7 0.2 - - - -
54A LEU* 3.0 27.4 + - - +
55A ASP 3.6 3.8 + - - -
63A ASN* 3.7 27.0 + - + +
66A LEU* 4.4 0.9 - - + -
67A LEU* 3.7 24.2 - - + -
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Residues in contact with VAL 13 (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 ASP 4.0 0.6 + - - -
12A VAL* 1.3 77.3 - - - +
14A GLU* 1.3 86.5 + - + +
15A GLY 3.2 0.9 - - - -
16A ARG* 2.9 25.5 + - - +
18A VAL* 3.4 30.0 - - + +
20A LEU* 6.1 0.4 - - + -
28A GLN* 4.1 19.3 - - - +
54A LEU* 3.7 14.4 - - + -
55A ASP* 3.6 6.7 - - - +
58A PHE* 5.4 0.2 - - + -
60A ARG* 3.4 31.4 - - - +
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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