Contacts of the strand formed by residues 376 - 383 (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 ILE 376 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B TYR* 3.5 32.5 - - + +
37B THR 3.3 3.8 - - - +
38B ASN* 3.8 12.8 - - - +
136B LEU* 3.6 36.6 - - + +
139B ILE* 3.6 32.3 - - + -
140B SER* 4.2 5.8 - - - +
180B ARG 5.4 1.1 - - - +
181B ARG* 2.9 31.4 + - - +
374B LEU* 3.6 28.5 - - + +
375B ASN* 1.3 74.3 - - - +
377B VAL* 1.3 65.3 + - - +
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Residues in contact with VAL 377 (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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36B TYR* 3.3 6.1 - - - -
37B THR* 2.9 52.5 + - - +
39B ARG* 3.6 47.6 - - - +
136B LEU* 3.9 6.5 - - - -
181B ARG* 4.0 7.0 - - - +
376B ILE* 1.3 80.3 - - - +
378B ILE* 1.3 66.3 - - - +
379B LYS* 4.6 17.0 - - + +
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Residues in contact with ILE 378 (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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34B TYR* 3.7 32.3 - - + -
35B LYS 3.5 6.5 - - - +
36B TYR* 4.0 17.5 - - + +
119B ILE* 5.1 4.3 - - + -
121B VAL* 5.0 7.6 - - + -
131B TYR* 6.3 0.4 - - + -
132B GLU* 3.6 42.7 + - + +
135B LEU* 3.6 39.5 - - + -
136B LEU* 3.9 24.8 - - + +
139B ILE* 4.6 8.1 - - + -
377B VAL* 1.3 80.6 - - - +
379B LYS* 1.3 58.0 + - - +
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Residues in contact with LYS 379 (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* 3.3 30.3 + - - -
34B TYR* 3.1 4.8 - - - -
35B LYS* 2.8 47.9 + - + +
37B THR* 3.6 20.2 - - - +
39B ARG* 5.8 1.6 - - - +
377B VAL* 4.6 15.9 - - + -
378B ILE* 1.3 73.6 - - - +
380B LEU* 1.3 68.8 + - - +
381B LEU* 3.3 21.8 + - + +
399B MSE 4.0 40.8 - - + +
400B GLY* 5.1 7.7 - - - +
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Residues in contact with LEU 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B VAL* 3.8 28.0 - - + -
33B THR 3.7 15.7 - - - +
34B TYR* 3.6 29.2 - - + +
125B TRP* 4.7 5.4 - - + +
233B GLU* 3.9 35.2 - - + +
236B MSE 3.8 22.4 - - + +
237B GLY* 4.0 9.6 - - - +
379B LYS* 1.3 77.6 - - - +
381B LEU* 1.4 57.2 + - - +
382B GLU 3.8 5.6 - - - +
383B VAL* 3.9 15.7 - - + -
388B ALA* 3.8 23.7 - - + +
399B MSE 5.0 2.3 - - - +
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Residues in contact with LEU 381 (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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363A LYS* 6.6 0.7 - - - -
33B THR* 2.8 34.2 + - + +
35B LYS* 4.2 39.7 - - + -
120B LEU* 4.7 4.3 - - + -
379B LYS* 3.3 19.7 + - - +
380B LEU* 1.4 73.5 - - - +
382B GLU* 1.3 68.8 + - + +
387B HIS* 3.8 9.0 + - - +
388B ALA* 3.0 25.6 + - - +
400B GLY* 6.3 3.1 - - - -
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Residues in contact with GLU 382 (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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42A GLN* 4.2 19.3 - - - +
43A LEU* 6.2 0.3 - - - +
111A LYS* 4.4 2.9 + - - -
32B VAL* 3.3 5.2 - - - +
33B THR* 3.0 33.3 + - - +
380B LEU* 3.8 1.0 - - - +
381B LEU* 1.3 88.8 - - + +
383B VAL* 1.3 66.3 + - - +
385B GLY* 3.6 26.3 - - - +
386B ASN 3.1 18.2 - - - +
387B HIS* 4.6 10.9 + - - +
388B ALA* 4.3 0.9 - - - +
503B EDO 3.2 29.0 + - - +
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Residues in contact with VAL 383 (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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30B VAL* 3.4 30.3 - - + -
31B THR 3.4 4.9 - - - +
32B VAL* 4.3 3.8 - - + -
125B TRP* 5.4 1.3 - - + -
237B GLY* 4.2 9.9 - - - +
240B SER* 3.7 22.6 - - - +
241B ILE* 3.8 21.5 - - + +
380B LEU* 3.9 30.1 - - + -
382B GLU* 1.3 79.9 - - - +
384B ASN* 1.3 72.1 + - - +
386B ASN* 2.8 27.6 + - - +
388B ALA* 4.2 2.5 - - + -
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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