Contacts of the strand formed by residues 5 - 11 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4C LYS* 1.3 74.9 - - - +
6C ILE* 1.4 66.3 + - - +
33C ASN* 3.0 35.5 + - - +
35C VAL* 3.8 8.7 - - + -
53C THR* 3.7 32.4 + - - +
54C LYS 4.5 1.1 - - - -
55C ALA* 3.9 15.9 - - + -
56C ASP* 2.9 39.3 + - - +
57C ALA 3.5 3.8 + - - -
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Residues in contact with ILE 6 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C THR* 1.4 81.2 - - - +
7C VAL* 1.3 59.9 + - - +
8C LEU* 4.6 8.7 - - + -
27C PHE* 3.7 33.2 - - + -
32C PHE* 4.0 11.4 - - + -
33C ASN 2.9 8.7 + - - +
34C VAL* 4.0 28.9 - - + -
35C VAL* 2.8 34.3 + - - +
56C ASP* 5.7 0.9 - - + -
57C ALA* 3.3 17.0 - - + +
59C LEU* 4.0 18.8 - - + -
130C LEU* 3.5 27.8 - - + -
134C LEU* 5.7 0.7 - - + -
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Residues in contact with VAL 7 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C ILE* 1.3 75.5 - - - +
8C LEU* 1.3 62.2 + - - +
35C VAL* 3.3 11.0 - - + +
37C ILE* 4.2 8.1 - - + -
46C PHE* 3.9 35.4 - - + +
49C ALA* 3.8 17.0 - - + +
50C ALA* 3.5 40.6 - - + +
53C THR* 4.3 3.6 - - - +
55C ALA* 3.9 9.0 - - + -
57C ALA 3.0 10.0 + - - +
58C ILE* 3.6 7.3 - - + -
59C LEU* 2.8 30.0 + - - +
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Residues in contact with LEU 8 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C ILE* 4.6 7.0 - - + -
7C VAL* 1.3 75.8 - - - +
9C GLY* 1.3 67.6 + - - +
20C ASN* 3.8 23.3 - - - +
23C LEU* 4.0 26.9 - - + -
24C ASP* 3.7 36.3 - - + +
27C PHE* 6.0 0.2 - - + -
34C VAL* 3.9 21.5 - - + -
35C VAL 2.9 7.0 + - - +
36C ASN* 3.2 6.2 - - - +
37C ILE* 2.9 29.8 + - - +
46C PHE* 4.4 1.1 - - - -
59C LEU* 3.5 27.6 - - + +
61C SER* 5.4 3.1 - - - -
800C CNC 5.8 0.7 - - + -
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Residues in contact with GLY 9 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C LEU* 1.3 78.1 - - - +
10C VAL* 1.3 65.1 + - - -
20C ASN* 4.1 9.0 - - - -
37C ILE* 3.9 2.9 - - - -
38C GLY 3.4 12.6 - - - -
46C PHE* 3.7 16.9 - - - -
59C LEU 3.3 7.6 + - - +
61C SER* 3.0 29.5 + - - -
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Residues in contact with VAL 10 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C GLY* 1.3 78.1 - - - +
11C ILE* 1.3 60.5 + - - +
14C ASP* 3.4 42.2 - - + +
16C HIS 3.5 20.9 - - - +
20C ASN* 4.0 20.2 - - + +
38C GLY 3.0 5.1 + - - -
39C VAL* 3.9 18.6 - - + -
40C LEU 3.2 6.1 + - - -
41C SER* 3.0 25.1 + - - -
46C PHE* 4.0 2.4 - - - -
61C SER* 3.2 22.2 - - - +
63C LEU* 4.7 6.5 - - + -
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Residues in contact with ILE 11 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C VAL* 1.3 74.1 - - - +
12C GLY* 1.3 68.7 + - - +
13C SER 3.7 0.3 + - - -
14C ASP* 3.3 19.9 - - - +
41C SER 3.2 12.6 - - - +
42C PRO* 4.9 0.2 - - + -
43C GLN* 4.1 20.2 - - + +
46C PHE* 3.9 16.3 - - + -
60C VAL* 3.9 27.6 - - + -
61C SER 3.1 15.0 + - - +
62C SER* 4.1 15.7 - - - +
64C TYR* 4.1 0.5 - - - -
70C ASP* 3.5 45.9 - - + +
71C CYS* 4.2 7.2 - - - -
74C LEU* 5.4 1.6 - - + -
113C TYR* 5.0 2.2 - - - +
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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