Contacts of the strand formed by residues 30 - 36 (chain A) in PDB entry 1WNA
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 LYS 30 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28A GLU 4.6 0.4 - - - +
29A ALA* 1.3 77.6 - - - +
31A VAL* 1.3 63.8 + - - +
32A TYR* 3.5 33.5 + - + +
50A LEU* 4.0 0.5 - - - +
51A HIS* 2.8 51.2 + - + +
88A ARG* 3.5 42.0 - - - +
90A TYR* 3.7 24.1 + - + +
115A MSE 6.0 2.5 - - - -
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Residues in contact with VAL 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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29A ALA* 5.1 1.1 - - + -
30A LYS* 1.3 75.9 - - - +
32A TYR* 1.3 64.8 + - - +
33A LEU* 4.7 6.7 - - + -
48A LEU* 3.6 24.0 - - + -
49A LEU 4.0 2.2 - - - -
50A LEU* 3.9 17.5 - - + -
78A VAL* 6.5 0.2 - - + -
81A LEU* 3.6 15.7 - - + -
86A ALA* 4.1 19.3 - - + -
88A ARG 2.9 12.2 + - - +
89A PHE* 3.6 32.9 - - + +
90A TYR* 2.8 29.7 + - - +
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Residues in contact with TYR 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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30A LYS* 3.5 46.9 + - + +
31A VAL* 1.3 74.0 - - - +
33A LEU* 1.3 62.9 + - - +
34A ILE* 3.8 1.7 + - + +
48A LEU* 3.5 5.4 - - - +
49A LEU* 2.9 60.8 + - + +
51A HIS* 4.0 14.9 - + + -
90A TYR* 3.6 34.4 - + + +
92A ALA* 5.9 0.2 - - + -
111A LEU* 4.7 2.9 - - + -
114A VAL* 3.7 31.2 - - + -
115A MSE 3.3 37.0 - - + +
118A ALA* 3.8 12.6 - - + -
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Residues in contact with LEU 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 VAL* 4.7 8.1 - - + +
32A TYR* 1.3 75.8 - - - +
34A ILE* 1.3 59.8 + - - +
35A THR 4.0 0.2 - - - -
46A TYR* 4.2 14.6 - - + -
47A ALA 3.5 11.0 - - - +
48A LEU* 4.3 17.0 - - + -
63A PHE* 6.1 0.2 - - + -
74A LEU* 4.5 16.4 - - + -
77A LEU* 4.8 8.5 - - + -
78A VAL* 4.5 10.5 - - + -
81A LEU* 6.2 0.7 - - + -
89A PHE* 4.9 8.3 - - + -
90A TYR 2.9 13.0 + - - +
91A GLU* 3.2 7.1 - - + +
92A ALA 2.9 23.9 + - - -
126A TYR* 3.1 54.5 - - + +
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Residues in contact with ILE 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 TYR 4.2 6.1 - - - +
33A LEU* 1.3 74.8 - - - +
35A THR* 1.3 61.9 + - - +
46A TYR* 3.2 5.1 - - - -
47A ALA* 2.8 43.2 + - + +
49A LEU* 4.2 21.1 - - + +
58A LEU* 4.7 3.6 - - + -
92A ALA* 3.4 12.1 - - + +
94A VAL* 4.5 6.3 - - + -
99A MSE 3.4 20.8 - - + +
102A LEU* 3.8 24.5 - - + -
103A LEU* 4.1 18.8 - - + -
110A LEU* 4.8 3.6 - - + -
114A VAL* 4.0 33.7 - - + -
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Residues in contact with THR 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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33A LEU 3.9 0.2 + - - -
34A ILE* 1.3 73.9 - - - +
36A ASP* 1.3 74.2 + - - +
41A ARG* 4.8 2.5 - - - +
44A ALA* 3.9 8.5 - - - +
45A ARG 2.8 21.8 + - - -
46A TYR* 3.5 20.5 - - + -
91A GLU* 3.7 29.8 - - - +
92A ALA 2.9 11.8 + - - +
93A VAL* 3.4 12.8 - - + -
94A VAL* 2.9 28.2 + - - +
99A MSE 3.8 5.4 - - - -
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Residues in contact with ASP 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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35A THR* 1.3 84.3 + - - +
37A TRP* 1.3 59.4 + - - +
38A GLN* 2.7 42.7 + - - +
43A GLN 4.7 1.2 - - - +
44A ALA* 3.9 2.8 - - - +
45A ARG* 3.2 49.1 + - + +
93A VAL* 4.3 2.6 - - - +
94A VAL* 3.2 10.1 - - + +
95A SER 4.7 0.7 - - - +
96A PRO* 4.1 19.6 - - + +
99A MSE 4.0 8.2 - - + +
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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