Contacts of the strand formed by residues 38 - 44 (chain B) in PDB entry 1VWJ
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 ALA 38 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B THR 3.8 0.8 - - - +
33B ALA* 3.4 6.1 - - - -
34B GLY* 2.9 26.4 + - - +
36B ASP* 3.1 22.8 + - - +
37B GLY* 1.3 80.9 - - - +
39B LEU* 1.3 63.0 + - - +
40B THR* 5.2 7.4 - - + -
58B GLY 3.8 3.8 - - - +
59B ARG* 3.6 13.7 - - - +
60B TYR* 3.6 2.1 - - - -
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Residues in contact with LEU 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B ILE* 4.0 9.4 - - + -
29B PHE* 5.1 2.0 - - + -
31B VAL* 3.4 27.8 - - + -
32B THR 3.6 1.6 - - - -
33B ALA* 3.8 14.6 - - + -
38B ALA* 1.3 81.6 - - - +
40B THR* 1.3 66.3 + - - +
56B LEU* 4.7 2.9 - - + -
57B THR* 3.3 7.0 + - - -
58B GLY* 2.9 43.0 + - - +
59B ARG* 3.8 9.6 - - - +
60B TYR* 3.7 19.7 - - + -
73B LEU* 4.3 17.3 - - + -
74B GLY 4.0 17.9 - - - +
75B TRP* 4.4 17.5 - - + -
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Residues in contact with THR 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B VAL* 3.5 2.9 - - - -
32B THR* 3.0 41.2 + - - -
38B ALA* 5.2 7.4 - - + -
39B LEU* 1.3 82.2 - - - +
41B GLY* 1.3 58.8 + - - +
56B LEU* 3.6 13.9 - - - +
57B THR* 4.7 8.1 - - - +
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Residues in contact with GLY 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B ILE* 3.0 15.0 - - - -
31B VAL* 4.3 0.2 - - - -
32B THR* 5.9 0.4 - - - -
40B THR* 1.3 78.0 - - - +
42B THR* 1.3 67.2 + - - -
55B VAL* 3.8 7.3 - - - +
56B LEU* 3.1 32.1 + - - +
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Residues in contact with THR 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B THR 3.9 0.5 - - - +
29B PHE* 3.5 0.5 - - - -
30B ILE* 2.9 45.5 + - - +
41B GLY* 1.3 78.4 + - - -
43B TYR* 1.3 60.5 + - - +
44B GLU* 5.0 2.0 - - + +
53B ARG* 3.5 41.1 - - + -
54B TYR 3.3 18.2 - - - +
55B VAL* 5.2 2.2 - - + +
56B LEU* 3.5 6.8 - - - +
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Residues in contact with TYR 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B ASN* 3.3 26.2 + - - -
27B SER* 3.7 23.2 + - - -
28B THR 3.3 5.4 - - - -
29B PHE* 3.8 24.9 - + + -
42B THR* 1.3 74.0 - - - +
44B GLU* 1.3 69.1 + - - +
52B SER 3.5 1.0 - - - +
53B ARG* 3.3 2.9 - - - -
54B TYR* 2.9 35.7 + - + +
56B LEU* 4.2 1.8 - - + -
75B TRP* 4.2 9.6 - - - -
77B VAL* 3.8 26.0 - - + -
79B TRP* 3.7 26.9 - + - -
92B TRP* 3.6 25.2 - + - -
128B ASP* 4.0 0.5 + - - -
130B PHE* 3.5 24.7 - + - -
4M PRO 5.0 2.5 - - - -
5M GLN* 5.1 4.8 - - + +
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Residues in contact with GLU 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B SER* 3.1 8.8 - - - -
28B THR* 2.7 54.2 + - + +
30B ILE* 3.7 24.0 - - + +
42B THR* 5.0 2.7 - - + -
43B TYR* 1.3 85.7 - - - +
45B SER* 1.3 70.3 + - - +
49B ASN 4.7 10.0 - - - +
50B ALA* 4.9 0.5 - - - +
52B SER* 3.1 8.5 - - - +
53B ARG* 3.5 43.1 + - + +
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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