Contacts of the strand formed by residues 376 - 383 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36D TYR* 3.5 32.8 - - + +
37D THR 3.4 2.5 - - - -
38D ASN* 3.7 17.3 - - - +
136D LEU* 3.6 46.4 - - + +
139D ILE* 3.8 22.2 - - + -
140D SER* 4.1 7.6 - - - +
180D ARG 5.2 0.7 - - - +
181D ARG* 3.3 27.4 + - + +
374D LEU* 3.3 29.9 + - + +
375D ASN* 1.3 75.9 + - - +
377D VAL* 1.3 65.2 + - - +
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Residues in contact with VAL 377 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35D LYS 5.3 0.4 - - - +
36D TYR* 3.4 5.4 - - - -
37D THR* 2.9 51.6 + - - +
39D ARG* 3.6 37.7 - - - +
136D LEU* 3.8 8.3 - - - -
181D ARG* 3.7 12.3 - - - +
376D ILE* 1.3 81.6 - - - +
378D ILE* 1.3 65.1 + - - +
379D LYS* 3.6 36.3 - - + +
399D MSE 5.6 0.4 - - + -
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Residues in contact with ILE 378 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D TYR* 3.8 30.4 - - + -
35D LYS 3.3 7.6 - - - +
36D TYR* 4.0 16.8 - - + +
119D ILE* 5.1 4.0 - - + -
121D VAL* 5.0 7.4 - - + -
132D GLU* 3.6 48.7 + - + +
135D LEU* 3.5 41.3 - - + -
136D LEU* 3.8 18.8 - - + +
139D ILE* 4.7 7.0 - - + -
377D VAL* 1.3 77.5 - - - +
379D LYS* 1.3 68.5 + - - +
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Residues in contact with LYS 379 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D TYR* 3.7 6.5 - - - -
35D LYS* 2.8 33.6 + - - +
39D ARG* 4.5 2.7 - - - +
132D GLU* 5.3 5.8 - - - +
180D ARG* 5.7 5.2 - - - +
232D HIS* 6.4 1.6 - - - -
236D MSE 5.8 2.7 - - + -
377D VAL* 3.6 39.9 - - + -
378D ILE* 1.3 78.0 - - - +
380D LEU* 1.3 68.1 + - - +
381D LEU* 4.2 0.7 - - - +
390D LYS* 5.9 1.3 - - - +
399D MSE 3.6 42.8 - - + -
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Residues in contact with LEU 380 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32D VAL* 3.9 14.6 - - + -
33D THR 3.8 13.7 - - - +
34D TYR* 3.6 35.6 - - + +
125D TRP* 4.3 7.4 - - + +
233D GLU* 3.6 35.3 - - + +
236D MSE 3.8 30.9 - - + +
237D GLY* 4.1 8.7 - - - +
379D LYS* 1.3 78.1 - - - +
381D LEU* 1.3 58.7 + - - +
382D GLU 4.0 0.2 - - - +
383D VAL* 3.8 32.5 - - + -
388D ALA* 4.1 8.2 - - + +
399D MSE 5.3 3.6 - - - +
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Residues in contact with LEU 381 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D THR* 2.8 31.4 + - + +
35D LYS* 4.2 40.2 - - + -
120D LEU* 4.3 5.8 - - + -
379D LYS 3.3 0.8 + - - +
380D LEU* 1.3 74.0 - - - +
382D GLU* 1.3 68.2 + - + +
387D HIS* 3.9 9.8 + - - +
388D ALA* 3.0 26.6 + - - +
400D GLY* 6.2 4.5 - - - -
401D ASP 6.3 0.4 - - - +
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Residues in contact with GLU 382 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32D VAL* 3.3 2.9 - - - +
33D THR* 2.9 57.6 + - - +
380D LEU* 4.0 0.3 - - - +
381D LEU* 1.3 89.6 - - + +
383D VAL* 1.3 71.1 + - - +
384D ASN 4.4 0.2 - - - -
385D GLY* 4.1 18.3 + - - +
386D ASN 3.2 17.5 - - - +
387D HIS* 4.9 2.7 - - - +
388D ALA* 4.2 1.6 - - - +
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Residues in contact with VAL 383 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D VAL* 3.6 23.6 - - + -
31D THR 3.6 4.3 - - - -
32D VAL* 3.8 11.4 - - + -
125D TRP* 5.2 2.0 - - + -
237D GLY* 4.1 13.9 - - - +
240D SER* 3.6 20.5 - - - +
241D ILE* 3.7 18.4 - - + +
380D LEU* 3.8 29.2 - - + -
382D GLU* 1.3 79.5 - - - +
384D ASN* 1.3 70.2 + - + +
385D GLY 3.1 1.1 - - - -
386D ASN* 2.8 30.1 + - - +
388D ALA* 4.5 2.9 - - + +
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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