Contacts of the strand formed by residues 376 - 383 (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 ILE 376 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C TYR* 3.5 34.8 - - + +
37C THR 3.4 2.2 - - - -
38C ASN* 3.8 12.1 - - - +
136C LEU* 3.6 41.0 - - + +
139C ILE* 3.6 22.2 - - + -
140C SER* 3.9 9.4 - - - +
181C ARG* 3.0 32.2 + - + +
374C LEU* 3.4 34.2 + - + +
375C ASN* 1.3 74.6 + - - +
377C VAL* 1.3 65.1 - - - +
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Residues in contact with VAL 377 (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 5.2 0.4 - - - +
36C TYR* 3.3 5.9 - - - -
37C THR* 2.9 51.4 + - - +
39C ARG* 3.6 45.1 - - - +
136C LEU* 3.8 4.0 - - - -
181C ARG* 4.1 12.6 - - - +
375C ASN* 4.8 2.9 - - - +
376C ILE* 1.3 80.6 - - - +
378C ILE* 1.3 65.2 + - - +
379C LYS* 3.9 33.2 - - + +
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Residues in contact with ILE 378 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C TYR* 3.8 31.0 - - + -
35C LYS 3.4 8.1 - - - +
36C TYR* 3.9 19.1 - - + +
119C ILE* 5.3 4.3 - - + -
121C VAL* 5.0 7.6 - - + -
131C TYR* 6.3 0.2 - - + -
132C GLU* 3.5 43.3 + - + +
135C LEU* 3.6 38.1 - - + -
136C LEU* 3.8 24.8 - - + +
139C ILE* 4.7 6.3 - - + -
377C VAL* 1.3 79.5 - - - +
379C LYS* 1.3 65.5 + - - +
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Residues in contact with LYS 379 (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* 3.3 6.0 - - - -
35C LYS* 2.8 34.5 + - + +
39C ARG* 4.3 1.6 - - - +
132C GLU* 4.6 10.3 + - - +
180C ARG* 4.7 9.1 - - - +
181C ARG* 6.0 0.6 - - - +
232C HIS* 5.8 4.8 - - - -
236C MSE 6.0 2.0 - - + -
377C VAL* 3.9 37.6 - - + +
378C ILE* 1.3 83.0 - - - +
380C LEU* 1.3 67.4 + - - +
381C LEU* 3.3 0.5 + - - -
390C LYS* 5.2 7.6 - - - +
399C MSE 3.6 42.2 - - + -
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Residues in contact with LEU 380 (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* 3.8 25.4 - - + -
33C THR 3.8 14.1 - - - +
34C TYR* 3.6 31.1 - - + +
125C TRP* 4.3 7.9 - - + +
233C GLU* 3.7 38.0 - - + +
236C MSE 3.9 29.7 - - + +
237C GLY* 4.1 8.5 - - - +
379C LYS* 1.3 76.4 - - - +
381C LEU* 1.3 57.8 + - - +
382C GLU 4.1 0.4 - - - +
383C VAL* 3.8 24.7 - - + -
388C ALA* 4.0 8.1 - - + +
399C MSE 5.6 2.9 - - - +
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Residues in contact with LEU 381 (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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33C THR* 2.8 30.7 + - + +
35C LYS* 4.0 44.2 - - + +
120C LEU* 4.4 5.6 - - + -
379C LYS 3.3 1.0 + - - +
380C LEU* 1.3 74.8 - - - +
382C GLU* 1.3 61.5 + - + +
387C HIS* 4.0 8.3 + - - +
388C ALA* 3.1 25.7 + - - +
400C GLY* 6.0 5.8 - - - -
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Residues in contact with GLU 382 (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* 3.2 5.1 - - - +
33C THR* 2.9 45.5 + - - +
380C LEU* 3.9 0.5 - - - +
381C LEU* 1.3 86.2 - - + +
383C VAL* 1.3 66.7 + - - +
384C ASN 4.3 0.2 - - - -
385C GLY* 3.3 28.2 - - - +
386C ASN 3.2 24.3 - - - +
387C HIS* 5.0 7.2 + - - +
388C ALA* 4.1 1.3 - - - +
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Residues in contact with VAL 383 (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* 3.6 24.5 - - + -
31C THR 3.6 3.6 - - - -
32C VAL* 4.1 7.0 - - + -
125C TRP* 5.4 1.1 - - + -
237C GLY* 4.0 8.1 - - - +
240C SER* 3.2 27.2 - - - +
241C ILE* 3.7 21.1 - - + +
380C LEU* 3.8 31.2 - - + -
382C GLU* 1.3 78.1 - - - +
384C ASN* 1.3 73.5 + - - +
385C GLY 3.0 0.4 - - - -
386C ASN* 2.8 27.8 + - - +
388C ALA* 4.2 4.7 - - + -
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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