Contacts of the strand formed by residues 9 - 16 (chain A) in PDB entry 2WFJ
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 ARG 9 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A ARG 3.8 6.4 + - - +
8A PRO* 1.3 79.2 - - - +
10A CYS* 1.3 61.4 + - - +
25A VAL* 4.4 8.1 - - + -
26A PHE 3.1 11.9 - - - +
27A GLU* 4.3 19.0 + - + +
145A ILE* 3.8 28.7 - - + +
176A GLU* 3.4 9.6 - - - +
177A LEU* 2.9 47.0 + - + +
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Residues in contact with CYS 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 PRO* 4.3 0.9 - - - -
9A ARG* 1.3 79.5 - - - +
11A PHE* 1.3 63.0 + - - +
25A VAL* 3.3 6.4 - - - +
26A PHE* 2.8 36.4 + - + +
28A LEU* 3.9 15.5 - - + +
40A PHE* 4.2 10.3 - - + -
41A ARG* 3.9 39.3 - - - -
44A CYS* 3.8 17.7 - - - -
175A GLY 3.2 14.4 - - - +
176A GLU* 4.2 4.7 - - - +
177A LEU* 4.6 1.1 - - - +
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Residues in contact with PHE 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 CYS* 1.3 76.0 - - - +
12A PHE* 1.3 70.7 + - - +
13A ASP* 3.4 13.0 - - - -
23A ARG* 3.3 48.0 - - - +
24A VAL 3.1 11.0 - - - +
25A VAL* 4.2 6.1 - - + -
26A PHE* 4.6 1.6 - - - -
44A CYS* 4.5 1.0 - - - -
173A SER* 4.3 2.2 - - - -
174A CYS* 3.1 27.8 - - - +
175A GLY* 2.9 59.5 + - - +
176A GLU 3.8 5.8 - - - -
177A LEU* 3.5 29.6 - - + -
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Residues in contact with PHE 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 PHE* 1.3 87.0 - - - +
13A ASP* 1.3 62.9 + - - +
14A ILE* 3.9 16.5 + - + +
23A ARG* 3.3 3.3 - - - -
24A VAL* 2.8 37.4 + - + +
26A PHE* 3.7 26.0 - + - -
40A PHE* 3.6 20.9 - + - -
44A CYS* 3.8 12.6 - - - -
60A TYR* 3.8 22.4 - + + -
65A PHE* 3.8 15.7 - + - -
124A PHE* 3.5 33.9 - + - -
171A ILE* 3.7 24.9 - - + -
173A SER 3.5 3.8 - - - -
174A CYS* 3.8 9.0 - - + -
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Residues in contact with ASP 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 PHE* 3.4 7.9 - - - -
12A PHE* 1.3 71.5 - - - +
14A ILE* 1.3 55.7 + - - +
22A GLY 3.7 4.5 - - - +
23A ARG* 2.8 54.2 + - - +
171A ILE* 3.5 4.3 - - - -
172A LEU* 2.8 41.0 + - + +
173A SER* 2.7 37.5 + - - +
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Residues in contact with ILE 14 (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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12A PHE* 3.9 20.0 - - + +
13A ASP* 1.3 71.5 - - - +
15A ALA* 1.3 68.9 + - - +
16A ILE* 4.1 3.4 - - + -
20A PRO* 3.5 1.4 - - - +
21A ALA* 2.8 40.1 + - + -
22A GLY 2.9 15.9 + - - +
24A VAL* 4.2 11.7 - - + -
65A PHE* 3.7 31.4 - - + -
150A VAL* 3.9 20.9 - - + -
154A ILE* 4.2 11.0 - - + -
169A VAL* 4.1 15.9 - - + -
170A ARG 3.4 3.4 - - - +
171A ILE* 4.1 9.0 - - + -
172A LEU* 3.3 10.5 - - - +
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Residues in contact with ALA 15 (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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14A ILE* 1.3 74.6 - - - +
16A ILE* 1.3 65.7 + - - +
18A ASN* 3.9 19.1 - - - +
19A GLN 3.2 17.9 - - - +
20A PRO* 4.2 1.3 - - + -
21A ALA 4.2 0.2 - - - +
168A GLU 3.3 1.9 - - - +
169A VAL* 3.4 3.6 - - - -
170A ARG* 2.9 35.3 + - + +
172A LEU* 3.4 29.6 - - + +
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Residues in contact with ILE 16 (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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14A ILE* 4.1 8.7 - - + -
15A ALA* 1.3 78.5 - - - +
17A ASN* 1.3 70.9 + - + +
19A GLN* 2.9 26.9 + - - +
21A ALA* 4.1 11.7 - - + -
150A VAL 5.4 0.2 - - - +
153A GLU* 3.7 41.3 - - + +
154A ILE* 4.5 15.3 - - + -
157A GLN* 3.8 33.0 - - - +
167A ALA* 4.0 12.3 - - + -
168A GLU 3.3 3.6 - - - +
169A VAL* 4.3 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