Contacts of the strand formed by residues 27 - 34 (chain A) in PDB entry 2WJX
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 27 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A ASN 3.1 19.3 - - - +
26A SER* 1.3 71.8 - - - +
28A GLN* 1.3 63.4 + - - +
29A ILE* 3.4 3.9 + - + +
56A PHE* 4.6 2.0 - - + -
57A ARG 3.0 22.2 + - - +
58A LEU* 3.5 16.8 - - + -
59A THR 2.8 25.4 + - - -
86A TYR* 3.3 30.1 - - + -
311A PHE* 3.8 43.1 - - + -
315A ARG* 4.1 20.2 - - - +
321A ILE* 6.3 2.5 - - + -
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Residues in contact with GLN 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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26A SER* 3.5 26.9 + - - +
27A ILE* 1.3 73.3 - - - +
29A ILE* 1.3 62.2 + - - +
59A THR* 3.4 17.6 - - - +
61A HIS* 3.2 28.0 + - + -
83A ARG 6.1 0.7 - - - +
84A GLY 4.4 7.4 - - - +
85A VAL* 4.2 14.8 - - + +
86A TYR* 2.8 42.1 + - + +
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Residues in contact with ILE 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A ILE* 3.6 15.7 - - + +
28A GLN* 1.3 80.1 - - - +
30A GLY* 1.3 66.7 + - - +
44A PHE* 5.0 7.2 - - + -
48A MET* 5.5 0.2 - - - -
58A LEU* 3.5 25.6 - - + -
59A THR 3.1 39.6 + - - +
60A PRO* 3.2 15.2 - - + +
61A HIS* 2.8 28.8 + - - -
85A VAL* 3.8 6.1 - - - -
87A ALA* 3.4 19.7 - - + +
307A MET* 4.8 14.6 - - - -
311A PHE* 4.5 10.3 - - + -
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Residues in contact with GLY 30 (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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29A ILE* 1.3 81.5 - - - +
31A GLY* 1.3 58.0 - - - -
44A PHE* 5.4 0.5 - - - -
60A PRO* 5.4 0.9 - - - -
61A HIS 3.5 2.0 - - - -
80A GLN* 3.2 23.8 - - - -
85A VAL* 3.7 0.8 - - - +
87A ALA 3.0 11.3 + - - -
88A ILE* 3.3 14.9 - - - +
89A PHE* 2.8 29.0 + - - +
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Residues in contact with GLY 31 (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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30A GLY* 1.3 74.4 - - - -
32A LEU* 1.3 65.1 + - - +
33A PHE* 3.9 18.2 - - - -
44A PHE* 5.3 4.9 - - - -
60A PRO* 5.3 0.8 - - - +
61A HIS 2.9 12.4 + - - +
62A ILE* 3.4 7.0 - - - +
63A ASP 2.8 29.1 + - - +
80A GLN* 4.0 1.0 - - - +
89A PHE* 3.1 8.3 - - - -
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Residues in contact with LEU 32 (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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31A GLY* 1.3 77.7 - - - +
33A PHE* 1.3 61.9 + - - +
34A PRO* 4.0 0.5 - - - +
63A ASP* 3.6 22.9 - - + +
65A LEU* 4.1 16.8 - - + -
67A VAL* 5.0 0.6 - - + +
73A VAL* 4.6 8.5 - - + +
76A ALA* 4.0 21.8 - - + -
77A PHE* 4.4 10.8 - - + +
80A GLN* 3.9 18.2 - - + +
88A ILE* 4.2 11.2 - - + -
89A PHE 2.8 10.1 + - - +
90A GLY* 3.3 12.6 - - - -
91A PHE* 3.1 31.9 + - - +
100A ILE* 4.7 9.4 - - + -
111A PHE* 4.5 16.8 - - + -
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Residues in contact with PHE 33 (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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31A GLY* 4.0 17.3 - - - -
32A LEU* 1.3 75.6 - - - +
34A PRO* 1.3 71.7 - - + +
37A ALA* 4.4 10.5 - - + +
40A GLU* 4.0 5.4 - - + -
41A TYR* 3.7 48.0 - + + -
44A PHE* 3.7 26.2 - + - -
62A ILE* 4.1 13.0 - - + -
63A ASP 2.9 7.7 + - - -
64A ASN* 3.3 20.1 - - - +
65A LEU* 3.0 25.8 + - - +
67A VAL* 4.7 0.2 - - - -
89A PHE* 3.6 28.9 - + - -
91A PHE* 3.8 20.4 - + - -
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Residues in contact with PRO 34 (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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33A PHE* 1.3 89.6 - - + +
35A ARG* 1.3 70.5 + - - +
36A GLY 3.3 0.3 + - - -
37A ALA* 3.2 30.5 + - + +
64A ASN* 4.9 1.4 - - - +
65A LEU 3.4 9.2 - - - +
67A VAL* 4.0 21.3 - - + +
91A PHE* 3.4 44.0 - - + -
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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