Contacts of the strand formed by residues 31 - 38 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A GLY* 4.5 5.4 + - - +
111A LYS* 4.4 2.9 - - - +
29B ASP 3.5 9.1 + - - +
30B VAL* 1.3 75.1 - - - +
32B VAL* 1.3 70.5 + - - +
123B GLY* 3.3 19.7 - - - +
124B SER* 4.3 3.8 - - - +
383B VAL* 3.4 1.0 - - - -
384B ASN* 2.8 40.7 + - - +
503B EDO 2.7 28.7 + - - +
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Residues in contact with VAL 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B VAL* 4.2 5.4 - - + -
31B THR* 1.3 82.8 - - - +
33B THR* 1.3 63.1 + - - +
34B TYR* 3.7 17.3 - - + -
122B SER* 3.2 5.2 + - - -
123B GLY 2.8 33.0 + - - +
125B TRP* 3.5 37.2 - - + -
128B THR* 3.0 29.2 - - - +
380B LEU* 3.8 14.6 - - + -
382B GLU 3.3 11.4 - - - +
383B VAL* 4.3 6.1 - - + -
503B EDO 3.5 4.6 - - - -
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Residues in contact with THR 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A GLN* 4.2 4.5 + - - +
32B VAL* 1.3 71.3 - - - +
34B TYR* 1.3 71.5 - - - +
120B LEU* 4.1 24.7 - - + -
121B VAL 3.3 6.7 - - - +
122B SER* 2.8 22.3 + - - +
380B LEU* 3.7 3.0 - - - +
381B LEU* 2.8 40.1 + - + +
382B GLU* 3.0 22.2 + - - +
503B EDO 3.0 17.4 - - - -
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Residues in contact with TYR 34 (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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16B LYS* 4.6 5.8 - - - -
32B VAL* 3.7 9.9 - - + -
33B THR* 1.3 82.3 - - - +
35B LYS* 1.3 61.6 + - - +
119B ILE 4.0 0.2 - - - +
120B LEU* 3.4 4.9 - - - -
121B VAL* 2.8 46.5 + - + +
125B TRP* 3.1 17.2 + - - -
128B THR* 3.7 34.3 - - - -
129B ILE* 3.3 13.7 - - + +
132B GLU* 5.1 4.7 - - + -
233B GLU* 2.6 33.3 + - + -
378B ILE* 3.7 27.8 - - + -
379B LYS 3.1 7.9 - - - +
380B LEU* 3.6 33.0 - - + -
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Residues in contact with LYS 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A LYS* 5.6 5.4 - - - +
366A GLU* 5.1 2.0 + - - -
369A VAL* 3.9 31.0 - - - +
34B TYR* 1.3 75.6 - - - +
36B TYR* 1.3 73.5 + - - +
37B THR* 3.2 26.7 + - - +
118B LYS* 6.1 6.3 - - + +
119B ILE 3.6 5.2 - - - +
120B LEU* 3.8 22.4 - - + -
377B VAL 3.8 0.2 - - - +
378B ILE* 3.5 3.4 - - - -
379B LYS* 2.8 43.8 + - - +
381B LEU* 4.2 32.1 - - + -
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Residues in contact with TYR 36 (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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35B LYS* 1.3 91.8 + - - +
37B THR* 1.3 62.5 + - - +
38B ASN* 3.5 11.9 - - + +
45B PHE* 3.7 14.0 - - - -
117B LEU* 3.6 38.6 - - + -
118B LYS* 4.9 0.7 - - - -
119B ILE* 2.9 35.4 + - + +
136B LEU* 5.0 0.4 - - + -
139B ILE* 3.8 31.2 - - + -
376B ILE* 3.5 36.6 - - + +
377B VAL 3.3 13.9 - - - -
378B ILE* 4.0 13.2 - - + +
501B CL 3.1 26.7 - - + +
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Residues in contact with THR 37 (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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366A GLU* 3.6 22.0 - - - +
369A VAL* 4.4 15.7 - - + -
35B LYS* 3.2 19.2 + - - +
36B TYR* 1.3 76.9 - - - +
38B ASN* 1.3 72.5 + - - +
39B ARG* 3.7 13.7 + - + +
376B ILE* 3.3 3.8 - - - +
377B VAL* 2.9 46.4 + - - +
379B LYS* 3.6 19.0 + - - -
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Residues in contact with ASN 38 (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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368A GLN* 5.9 0.5 - - - +
369A VAL* 6.1 0.2 - - - +
36B TYR* 3.5 19.5 + - + +
37B THR* 1.3 76.1 - - - +
39B ARG* 1.3 61.1 + - - +
40B SER* 2.8 34.3 + - - -
41B SER* 3.9 16.5 + - - +
43B LEU 2.9 27.7 + - - -
45B PHE* 4.7 1.4 - - - -
374B LEU* 3.9 8.0 - - - +
375B ASN 3.6 4.6 - - - +
376B ILE* 3.8 11.5 - - - +
501B CL 3.4 21.3 - - + +
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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