Contacts of the strand formed by residues 31 - 38 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29C ASP 4.4 7.6 - - - +
30C VAL* 1.3 74.6 - - - +
32C VAL* 1.3 64.1 + - - +
123C GLY* 3.4 14.6 - - - +
124C SER* 4.7 7.4 - - - +
382C GLU 4.8 0.2 - - - -
384C ASN* 2.7 43.8 + - - +
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Residues in contact with VAL 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C VAL* 4.2 6.1 - - + -
31C THR* 1.3 80.4 - - - +
33C THR* 1.3 65.7 + - - +
34C TYR* 3.7 18.8 - - + -
122C SER* 3.3 1.2 - - - -
123C GLY 2.9 32.3 + - - +
125C TRP* 3.6 36.8 - - + -
128C THR* 3.1 28.3 - - - +
380C LEU* 3.8 7.2 - - + -
382C GLU* 3.2 10.8 - - - +
383C VAL* 4.1 17.5 - - + -
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Residues in contact with THR 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C VAL* 1.3 76.1 + - - +
34C TYR* 1.3 71.4 + - - +
120C LEU* 4.2 19.5 - - + -
121C VAL 3.2 4.0 - - - -
122C SER* 3.3 24.7 + - - +
380C LEU* 3.7 3.3 - - - +
381C LEU* 2.8 40.6 + - + -
382C GLU* 2.9 31.4 + - - +
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Residues in contact with TYR 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C LYS* 4.6 4.3 - - - -
32C VAL* 3.7 11.9 - - + -
33C THR* 1.3 80.9 - - - +
35C LYS* 1.3 60.8 + - - +
119C ILE 4.1 0.2 - - - +
120C LEU* 3.4 5.0 - - - -
121C VAL* 2.7 47.0 + - + +
125C TRP* 3.1 11.8 + - - -
128C THR* 3.5 34.5 - - - -
129C ILE* 3.2 15.2 - - - +
132C GLU* 5.3 4.7 - - + -
233C GLU* 2.3 42.9 + - + -
378C ILE* 3.8 25.4 - - + -
379C LYS* 3.3 9.4 - - - +
380C LEU* 3.6 29.8 - - + -
381C LEU* 4.7 0.2 - - - -
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Residues in contact with LYS 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C TYR* 1.3 74.9 - - - +
36C TYR* 1.3 76.6 + - - +
37C THR* 3.8 13.4 + - - +
119C ILE 3.7 3.6 - - - +
120C LEU* 3.7 19.1 - - + -
377C VAL* 3.8 0.7 - - - +
378C ILE* 3.4 4.1 - - - -
379C LYS* 2.8 34.8 + - - +
381C LEU* 4.0 36.2 - - + +
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Residues in contact with TYR 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C LYS* 1.3 87.6 - - - +
37C THR* 1.3 66.1 + - - +
38C ASN* 3.5 16.0 - - + +
45C PHE* 3.6 14.2 - - - -
117C LEU* 3.6 39.9 - - + +
118C LYS* 4.8 0.6 - - - -
119C ILE* 3.0 37.0 + - + +
136C LEU* 4.8 0.7 - - + -
139C ILE* 3.9 28.3 - - + -
376C ILE* 3.5 31.9 - - + +
377C VAL 3.3 14.6 - - - -
378C ILE* 3.9 14.3 - - + +
501C CL 3.0 27.6 - - + +
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Residues in contact with THR 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C LYS* 3.8 14.6 + - - +
36C TYR* 1.3 81.5 + - - +
38C ASN* 1.3 71.7 + - - +
39C ARG* 3.6 14.7 + - + +
375C ASN 4.1 0.2 - - - +
376C ILE* 3.4 3.1 - - - +
377C VAL* 2.9 46.1 + - - +
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Residues in contact with ASN 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C TYR* 3.5 19.9 + - + +
37C THR* 1.3 77.0 - - - +
39C ARG* 1.3 59.8 + - - +
40C SER* 2.7 35.7 + - - -
41C SER* 3.9 14.5 + - - +
43C LEU 3.0 27.7 + - - -
45C PHE* 4.6 1.2 - - - -
374C LEU* 3.9 8.2 - - - +
375C ASN 3.7 2.3 - - - +
376C ILE* 3.8 13.8 - - - +
501C CL 3.3 20.8 - - + +
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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