Contacts of the strand formed by residues 31 - 38 (chain A) in PDB entry 1VLP
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 THR 31 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A ASP 3.7 10.5 - - - +
30A VAL* 1.3 76.4 - - - +
32A VAL* 1.3 71.3 + - - +
122A SER* 6.0 0.4 - - - -
123A GLY* 3.3 15.0 - - - +
124A SER* 4.4 6.7 - - - +
383A VAL* 3.4 0.7 - - - -
384A ASN* 2.9 46.4 + - - +
385A GLY 5.1 0.5 + - - -
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Residues in contact with VAL 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 VAL* 4.2 0.4 - - + -
31A THR* 1.3 82.4 - - - +
33A THR* 1.3 62.7 + - - +
34A TYR* 3.7 16.4 - - + -
122A SER* 3.1 7.3 + - - -
123A GLY 2.8 34.0 + - - +
125A TRP* 3.6 36.8 - - + -
128A THR* 2.9 29.4 - - - +
380A LEU* 3.8 14.1 - - + -
382A GLU 3.2 12.8 - - - +
383A VAL* 4.1 13.7 - - + -
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Residues in contact with THR 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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32A VAL* 1.3 72.0 + - - +
34A TYR* 1.3 75.4 + - - +
120A LEU* 4.0 22.4 - - + -
121A VAL 3.2 7.9 - - - +
122A SER* 2.9 24.3 + - - -
380A LEU* 3.7 3.0 - - - +
381A LEU* 2.9 35.2 + - + +
382A GLU* 2.9 34.7 + - - +
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Residues in contact with TYR 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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16A LYS* 4.6 5.2 - - - -
32A VAL* 3.7 9.4 - - + -
33A THR* 1.3 83.1 - - - +
35A LYS* 1.3 60.9 + - - +
119A ILE 4.1 0.2 - - - +
120A LEU* 3.4 5.4 - - - -
121A VAL* 2.8 46.0 + - + +
125A TRP* 3.0 18.7 + - - -
128A THR* 3.5 35.0 - - - -
129A ILE* 3.7 12.5 - - - -
131A TYR* 6.4 0.2 - - + -
132A GLU* 5.3 5.6 - - + -
233A GLU* 2.3 40.3 + - + -
378A ILE* 3.7 27.4 - - + -
379A LYS 3.1 7.6 - - - +
380A LEU* 3.6 29.8 - - + -
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Residues in contact with LYS 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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34A TYR* 1.3 75.6 - - - +
36A TYR* 1.3 74.0 + - - +
37A THR* 2.7 33.9 + - - +
119A ILE 3.7 5.4 - - - +
120A LEU* 3.8 18.4 - - + -
377A VAL 3.9 0.3 - - - +
378A ILE* 3.3 4.3 - - - -
379A LYS* 2.9 46.2 + - - +
381A LEU* 3.9 33.8 - - + +
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Residues in contact with TYR 36 (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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35A LYS* 1.3 87.4 + - - +
37A THR* 1.3 68.0 + - - +
38A ASN* 3.6 11.1 - - + +
45A PHE* 3.8 12.8 - - - -
117A LEU* 3.5 40.5 - - + +
118A LYS* 4.9 0.2 - - - -
119A ILE* 3.1 34.2 + - + +
136A LEU* 4.9 0.7 - - + -
139A ILE* 3.8 29.5 - - + +
376A ILE* 3.5 37.1 - - + +
377A VAL 3.3 13.9 - - - -
378A ILE* 3.9 12.6 - - + +
501A CL 3.1 27.0 - - + +
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Residues in contact with THR 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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35A LYS* 2.7 28.3 + - - +
36A TYR* 1.3 78.4 + - - +
38A ASN* 1.3 72.0 + - - +
39A ARG* 3.7 13.4 + - + +
376A ILE* 3.3 4.5 - - - +
377A VAL* 2.9 45.7 + - - +
379A LYS* 3.6 19.8 + - - +
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Residues in contact with ASN 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 TYR* 3.6 19.3 + - + +
37A THR* 1.3 77.3 - - - +
39A ARG* 1.3 61.7 + - - +
40A SER* 2.9 31.4 + - - +
41A SER* 3.8 17.4 + - - +
43A LEU 3.0 27.5 + - - -
45A PHE* 4.7 1.0 - - - -
374A LEU* 4.0 9.2 - - - +
375A ASN 3.6 3.8 - - - +
376A ILE* 3.7 14.8 - - - +
501A CL 3.4 21.1 - - + +
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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