Contacts of the strand formed by residues 32 - 39 (chain A) in PDB entry 2WIN
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 PRO 32 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A ASP* 4.5 3.6 - - + +
31A VAL* 1.3 83.3 - - + +
33A VAL* 1.3 57.2 + - - +
34A THR* 5.1 7.2 - - + +
53A VAL* 4.2 16.8 - - + -
89A THR 3.5 1.0 - - - +
90A PHE 3.6 0.2 - - - -
91A GLY* 2.7 43.8 + - - -
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Residues in contact with VAL 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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22A LEU* 3.6 38.1 - - + -
31A VAL* 3.4 18.2 - - + +
32A PRO* 1.3 74.8 - - - +
34A THR* 1.3 67.1 + - - +
35A VAL* 4.4 5.2 - - + -
51A LYS* 3.3 6.4 - - - +
52A THR 2.8 43.0 + - - +
54A LEU* 3.7 25.4 - - + -
89A THR 3.4 10.1 - - - +
90A PHE* 3.7 23.6 - - + -
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Residues in contact with THR 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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32A PRO* 5.1 5.4 - - + +
33A VAL* 1.3 79.9 - - - +
35A VAL* 1.3 63.7 + - - +
36A THR* 4.3 6.8 + - - -
51A LYS* 3.7 32.3 - - + -
87A GLN 3.4 4.3 - - - +
89A THR* 2.9 49.5 + - - +
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Residues in contact with VAL 35 (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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20A MET* 3.5 43.1 - - + -
22A LEU* 3.9 20.2 - - + -
33A VAL* 4.1 2.2 - - + -
34A THR* 1.3 73.0 - - - +
36A THR* 1.3 74.3 + - - +
37A VAL* 4.8 7.2 - - + -
47A LEU* 4.6 3.4 - - + +
48A SER 3.4 4.2 - - - +
49A SER 2.9 25.7 - - - +
50A GLU* 3.4 21.1 + - + +
64A VAL* 3.9 20.4 - - + -
66A PHE* 5.6 4.3 - - + -
86A VAL* 4.7 2.5 - - + -
87A GLN 3.6 3.6 - - - +
88A ALA* 4.3 2.9 - - + -
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Residues in contact with THR 36 (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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34A THR* 4.3 8.1 + - - -
35A VAL* 1.3 78.4 + - - +
37A VAL* 1.3 68.5 + - - +
38A HIS* 3.3 30.7 - - + -
45A LEU* 3.6 15.3 - - + -
47A LEU* 3.5 12.8 - - - +
48A SER* 3.8 11.1 + - - -
86A VAL* 4.4 0.5 - - - +
87A GLN* 2.7 50.1 + - - +
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Residues in contact with VAL 37 (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 LEU* 5.7 0.2 - - + -
35A VAL* 4.8 8.7 - - + -
36A THR* 1.3 80.6 - - - +
38A HIS* 1.3 69.4 + - - +
45A LEU* 3.9 1.4 - - - -
46A VAL* 3.2 39.7 + - + +
47A LEU* 2.8 29.7 + - + +
66A PHE* 4.6 23.3 - - + -
68A ILE* 4.9 9.0 - - + -
84A VAL* 4.1 27.8 - - + -
85A THR 3.6 6.5 - - - +
86A VAL* 4.7 14.4 - - + +
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Residues in contact with HIS 38 (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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36A THR* 3.3 23.0 - - + +
37A VAL* 1.3 74.2 - - - +
39A ASP* 1.3 69.1 + - - +
42A GLY 4.3 8.3 - - - +
43A LYS* 3.2 30.0 + - + -
44A LYS 4.4 3.6 - - - -
45A LEU* 3.3 45.8 - - + +
46A VAL* 4.3 5.8 - - - -
84A VAL* 3.5 6.1 - - - +
85A THR* 2.8 42.8 + - - +
87A GLN* 3.6 26.7 + - - -
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Residues in contact with ASP 39 (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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38A HIS* 1.3 76.5 - - - +
40A PHE* 1.3 61.4 + - - +
41A PRO 3.6 9.6 - - - +
42A GLY 3.1 19.1 - - - +
43A LYS 3.5 5.1 + - - -
44A LYS* 3.0 52.4 + - + +
45A LEU 4.7 0.2 - - - +
46A VAL* 4.4 14.9 - - + +
83A PHE 4.4 4.0 - - - +
84A VAL* 4.7 5.8 - - + +
85A THR* 4.5 3.3 + - - -
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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