Contacts of the strand formed by residues 5 - 11 (chain A) in PDB entry 1CCW
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 THR 5 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3A LYS* 5.5 1.2 - - - +
4A LYS* 1.3 71.8 - - - +
6A ILE* 1.3 66.9 + - - +
33A ASN* 3.1 37.9 + - - +
35A VAL* 3.8 8.5 - - + -
53A THR* 3.8 34.7 + - - +
54A LYS 4.4 1.1 - - - -
55A ALA* 3.9 11.4 - - + -
56A ASP* 2.9 45.9 + - - +
57A ALA 3.4 1.4 + - - -
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Residues in contact with ILE 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 LYS* 5.8 0.4 - - + -
5A THR* 1.3 81.1 - - - +
7A VAL* 1.3 61.2 + - - +
8A LEU* 4.5 10.5 - - + -
27A PHE* 3.9 34.1 - - + -
32A PHE* 4.1 13.2 - - + -
33A ASN 3.0 7.6 + - - +
34A VAL* 4.1 24.2 - - + -
35A VAL* 2.8 34.0 + - - +
55A ALA* 4.5 0.2 - - - -
56A ASP* 5.6 0.4 - - + -
57A ALA* 3.3 16.2 - - + +
59A LEU* 3.9 21.3 - - + -
130A LEU* 3.6 28.5 - - + -
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Residues in contact with VAL 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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6A ILE* 1.3 75.5 - - - +
8A LEU* 1.3 58.2 + - - +
35A VAL* 3.4 11.9 - - + +
37A ILE* 4.2 8.5 - - + -
46A PHE* 4.0 26.5 - - + +
49A ALA* 3.7 23.1 - - + +
50A ALA* 3.5 37.5 - - + +
53A THR* 4.3 3.4 - - - +
55A ALA* 3.8 11.4 - - + -
57A ALA 3.0 9.6 + - - +
58A ILE* 3.5 8.0 - - + +
59A LEU* 2.7 35.2 + - - +
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Residues in contact with LEU 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 ILE* 4.5 7.4 - - + -
7A VAL* 1.3 74.3 - - - +
9A GLY* 1.3 67.2 + - - +
20A ASN* 3.8 22.9 - - - +
23A LEU* 3.9 28.5 - - + +
24A ASP* 3.7 36.6 - - + +
27A PHE* 6.1 0.4 - - + -
34A VAL* 4.0 19.3 - - + -
35A VAL 3.0 5.6 + - - +
36A ASN* 3.3 6.1 - - - +
37A ILE* 2.8 30.7 + - - +
46A PHE* 4.4 0.9 - - - -
59A LEU* 3.5 28.0 - - + +
61A SER* 5.3 2.9 - - - -
800A CNC 5.8 0.9 - - + -
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Residues in contact with GLY 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 LEU* 1.3 78.7 - - - +
10A VAL* 1.3 64.1 + - - -
20A ASN* 4.1 8.1 - - - -
37A ILE* 3.8 3.4 - - - -
38A GLY 3.4 12.6 - - - -
46A PHE* 3.7 16.8 - - - -
59A LEU 3.3 7.3 + - - +
61A SER* 2.9 29.3 + - - -
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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 GLY* 1.3 77.4 - - - +
11A ILE* 1.3 61.8 + - - +
14A ASP* 3.5 39.5 - - + +
16A HIS 3.5 21.5 - - - +
20A ASN* 4.0 22.9 - - + +
38A GLY 3.0 5.3 + - - +
39A VAL* 3.9 15.5 - - + -
40A LEU 3.3 5.8 + - - -
41A SER* 3.1 25.3 + - - -
46A PHE* 4.0 1.5 - - - -
61A SER* 3.3 21.5 - - - +
63A LEU* 4.4 7.4 - - + -
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Residues in contact with ILE 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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10A VAL* 1.3 75.6 - - - +
12A GLY* 1.3 68.2 + - - +
13A SER 3.6 0.2 + - - -
14A ASP* 3.3 20.0 - - - +
41A SER 3.2 12.3 - - - +
42A PRO* 4.9 0.4 - - + -
43A GLN* 4.0 20.6 - - + +
46A PHE* 3.9 11.8 - - + -
60A VAL* 3.9 27.4 - - + -
61A SER 3.1 14.7 + - - +
62A SER* 4.0 16.4 - - - +
64A TYR* 4.1 0.7 - - - -
70A ASP* 3.5 44.7 - - + +
71A CYS* 4.3 7.9 - - - -
74A LEU* 5.4 1.8 - - + -
113A TYR* 5.1 2.7 - - - +
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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