Contacts of the strand formed by residues 19 - 28 (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 GLN 19 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A ALA* 3.9 2.0 - - - -
16A ILE* 2.9 32.4 + - + +
17A ASN 3.1 5.1 + - - +
18A ASN* 1.3 78.1 - - - +
20A PRO* 1.3 81.9 - - + +
21A ALA* 3.2 1.7 + - - +
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Residues in contact with PRO 20 (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 3.5 8.5 - - - +
15A ALA* 4.1 4.9 - - + -
18A ASN 3.6 9.4 - - - +
19A GLN* 1.3 94.9 - - + +
21A ALA* 1.3 60.6 + - - +
22A GLY 4.9 2.5 - - - +
172A LEU* 5.0 8.7 - - + -
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Residues in contact with ALA 21 (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* 2.8 22.4 + - + +
16A ILE* 4.1 24.7 - - + -
19A GLN 3.2 1.9 + - - +
20A PRO* 1.3 72.6 - - - +
22A GLY* 1.3 58.9 + - - +
150A VAL* 3.5 19.7 - - + +
153A GLU* 4.0 23.7 - - - +
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Residues in contact with GLY 22 (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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13A ASP* 4.5 3.4 - - - -
14A ILE* 2.9 33.5 + - - +
20A PRO* 3.7 3.2 - - - +
21A ALA* 1.3 79.6 - - - +
23A ARG* 1.3 61.4 + - - -
150A VAL* 3.9 9.2 - - - -
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Residues in contact with ARG 23 (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* 3.3 32.6 - - + -
12A PHE 3.3 8.3 - - - +
13A ASP* 2.8 39.9 + - - +
22A GLY* 1.3 73.7 - - - -
24A VAL* 1.3 71.7 + - - +
25A VAL* 3.9 16.1 + - + +
146A SER* 3.9 2.3 + - - +
147A GLY* 3.3 21.7 + - - -
149A GLU* 5.1 0.3 - - - +
150A VAL* 4.1 2.1 - - - +
177A LEU* 3.9 24.4 - - - +
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Residues in contact with VAL 24 (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* 3.1 4.9 - - - +
12A PHE* 2.8 38.8 + - + +
14A ILE* 4.2 11.2 - - + -
23A ARG* 1.3 74.9 - - - +
25A VAL* 1.3 63.3 + - - +
26A PHE* 3.6 34.5 - - + -
65A PHE* 6.3 1.1 - - + -
126A ILE* 4.9 1.3 - - + -
144A VAL* 4.0 12.8 - - + -
146A SER 3.5 9.2 - - - +
147A GLY 3.8 4.9 - - - +
150A VAL* 3.8 30.3 - - + -
151A VAL* 4.1 17.5 - - + -
154A ILE* 5.5 2.0 - - + -
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Residues in contact with VAL 25 (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 ARG* 4.4 3.4 - - + -
10A CYS 3.3 10.8 - - - +
11A PHE* 4.2 4.0 - - + -
23A ARG* 3.9 24.5 - - + +
24A VAL* 1.3 78.0 - - - +
26A PHE* 1.3 64.4 + - - +
144A VAL* 3.4 5.7 - - - +
145A ILE* 2.8 51.6 + - + -
146A SER* 2.9 30.7 + - - +
177A LEU* 3.8 24.2 - - + -
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Residues in contact with PHE 26 (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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8A PRO 4.0 0.2 - - - +
9A ARG* 3.1 8.3 - - - +
10A CYS 2.8 42.9 + - - +
12A PHE* 3.7 47.1 - + - -
24A VAL* 3.6 25.6 - - + -
25A VAL* 1.3 77.2 - - - +
27A GLU* 1.3 60.0 + - - +
28A LEU* 4.1 18.1 - - + +
40A PHE* 4.0 15.5 - + + -
110A LEU* 3.9 24.2 - - + -
126A ILE* 3.7 25.1 - - + -
143A GLN 3.3 10.3 - - - +
144A VAL* 3.9 17.7 - - + -
145A ILE* 4.4 2.5 - - - -
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Residues in contact with GLU 27 (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 ARG* 3.0 53.3 + - + +
8A PRO 3.6 5.8 - - - +
9A ARG* 4.3 22.1 + - + -
26A PHE* 1.3 73.3 - - - +
28A LEU* 1.3 65.0 + - - +
29A PHE* 4.2 9.4 - - + -
142A GLY* 3.1 4.0 - - - -
143A GLN* 2.9 33.1 + - + +
145A ILE* 3.9 27.0 - - + +
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Residues in contact with LEU 28 (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 ARG* 3.2 21.7 - - - +
8A PRO* 3.0 32.9 + - + +
10A CYS* 3.9 24.9 - - - -
26A PHE* 4.1 9.4 - - + +
27A GLU* 1.3 77.7 - - - +
29A PHE* 1.3 61.5 + - - +
30A SER 2.9 8.2 + - - -
37A CYS* 3.6 39.7 - - + +
40A PHE* 3.9 16.6 - - + -
41A ARG* 4.1 2.2 - - + -
110A LEU* 3.8 28.9 - - + -
141A PHE* 3.6 9.6 - - + +
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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