Contacts of the strand formed by residues 341 - 346 (chain B) in PDB entry 2VKM
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 PHE 341 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152B LEU 3.9 4.5 - - - +
153B GLN* 4.5 3.6 - - - -
154B LEU 4.8 0.5 + - - +
298B ILE* 3.6 20.6 - - + -
299B THR 3.4 22.9 - - - -
300B ILE* 3.5 19.3 - - + -
337B ILE* 3.0 42.2 - - + -
338B MET* 2.8 22.2 + - - +
339B GLU 3.4 0.4 - - - -
340B GLY* 1.3 88.5 - - - +
342B TYR* 1.3 65.1 + - - +
343B VAL* 3.7 13.1 + - + +
354B PHE* 4.3 13.5 - + + -
355B ALA 3.0 14.4 - - - +
356B VAL* 4.2 1.6 - - - -
357B SER* 3.6 10.4 + - - -
368B ALA* 4.2 1.8 - - + -
369B ALA 3.4 26.2 - - - -
370B VAL* 3.4 22.2 - - + -
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Residues in contact with TYR 342 (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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151B SER* 2.6 36.8 + - - -
152B LEU 3.5 20.2 - - - -
153B GLN* 4.0 5.2 - - + +
173B SER 5.5 0.2 - - - -
175B ILE* 3.8 1.0 - - - +
179B ILE* 3.4 23.5 - - + -
180B ASP 2.9 24.1 + - - -
183B LEU* 3.4 40.6 - - + +
184B TYR* 3.1 47.3 - + + -
188B LEU* 4.4 4.0 - - + +
341B PHE* 1.3 71.9 - - - +
343B VAL* 1.3 60.4 + - - +
344B VAL* 4.2 10.5 + - + -
353B GLY 3.6 0.9 - - - +
354B PHE* 3.6 4.0 - - - -
355B ALA* 2.8 27.7 + - + +
357B SER* 3.9 3.3 - - - -
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Residues in contact with VAL 343 (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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151B SER* 3.2 3.4 - - - -
152B LEU 2.7 39.6 + - - +
227B VAL* 4.6 2.7 - - + -
338B MET* 4.2 25.6 - - + -
341B PHE* 3.7 16.2 - - + +
342B TYR* 1.3 79.0 - - - +
344B VAL* 1.3 64.3 + - - +
345B PHE* 3.5 29.8 - - + -
352B ILE* 3.5 24.2 - - + -
353B GLY 3.3 4.0 - - - +
354B PHE* 4.1 23.6 - - + -
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Residues in contact with VAL 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B LEU* 4.1 17.0 - - + -
150B PHE 3.9 2.0 - - - -
151B SER* 4.0 12.6 - - - -
179B ILE* 4.0 34.3 - - + -
188B LEU* 4.1 25.6 - - + -
190B TYR* 4.2 7.4 - - + +
342B TYR* 4.2 9.6 - - + -
343B VAL* 1.3 75.3 - - - +
345B PHE* 1.3 61.7 + - - +
346B ASP* 3.2 14.6 + - + +
352B ILE* 3.1 8.7 - - - +
353B GLY* 2.8 42.2 + - - +
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Residues in contact with PHE 345 (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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33B THR* 3.8 16.2 - - + -
149B LEU* 3.5 1.7 - - - -
150B PHE* 2.8 63.8 + + + +
152B LEU* 4.0 11.4 - - + -
193B ILE* 5.7 0.4 - - - -
199B TYR* 3.6 50.0 - + + -
227B VAL* 3.7 26.2 - - + -
338B MET* 3.9 13.9 - - + -
343B VAL* 3.5 26.2 - - + -
344B VAL* 1.3 72.5 - - - +
346B ASP* 1.3 58.7 + - - +
347B ARG* 2.9 12.4 + - - +
351B ARG 3.9 2.7 - - - -
352B ILE* 3.9 17.0 - - + -
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Residues in contact with ASP 346 (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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149B LEU* 3.9 27.0 - - + +
190B TYR* 4.3 4.3 + - + -
193B ILE* 4.9 0.9 - - - -
344B VAL* 3.2 9.5 + - + -
345B PHE* 1.3 69.1 - - - +
347B ARG* 1.3 57.8 + - - +
348B ALA* 3.4 8.7 + - - +
349B ARG* 2.9 28.2 + - - +
350B LYS 2.9 19.4 + - - -
351B ARG* 2.8 65.1 + - + +
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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
------------------------------------------------------------
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