Contacts of the strand formed by residues 341 - 346 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152D LEU 3.9 5.4 - - - +
153D GLN* 4.5 4.0 - - - -
154D LEU 4.7 0.3 + - - -
298D ILE* 3.6 26.2 - - + -
299D THR 3.5 23.1 - - - -
300D ILE* 3.5 18.8 - - + -
337D ILE* 3.2 34.3 - - + -
338D MET* 2.9 17.6 + - - +
339D GLU 3.4 0.8 - - - -
340D GLY* 1.3 92.8 - - - +
342D TYR* 1.3 67.5 + - - +
343D VAL* 3.8 11.9 + - + +
354D PHE* 4.3 12.6 - + + -
355D ALA 3.2 13.0 - - - +
356D VAL* 4.1 1.6 - - - -
357D SER* 3.6 12.1 - - - -
368D ALA* 4.1 5.6 - - + -
369D ALA 3.4 22.7 - - - -
370D VAL* 3.5 22.0 - - + -
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Residues in contact with TYR 342 (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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151D SER* 2.7 36.4 + - - -
152D LEU 3.5 21.5 - - - -
153D GLN* 3.9 5.2 - - + +
175D ILE* 4.0 0.7 - - - +
179D ILE* 3.4 23.9 - - + -
180D ASP 3.0 23.0 + - - -
183D LEU* 3.6 40.6 - - + +
184D TYR* 3.4 40.2 - + + -
188D LEU* 4.4 4.9 - - + +
341D PHE* 1.3 72.6 - - - +
343D VAL* 1.3 60.1 + - - +
344D VAL* 4.2 10.9 + - + -
353D GLY 3.6 0.5 - - - +
354D PHE* 3.5 5.2 - - - -
355D ALA* 2.7 33.0 + - + +
357D SER* 3.9 2.6 - - - -
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Residues in contact with VAL 343 (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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151D SER* 3.3 3.2 - - - -
152D LEU 2.8 38.9 + - - +
227D VAL* 4.5 2.7 - - + -
338D MET* 4.1 26.5 - - + +
341D PHE* 4.0 15.5 - - + +
342D TYR* 1.3 78.3 - - - +
344D VAL* 1.3 63.9 + - - +
345D PHE* 3.6 28.1 - - + -
352D ILE* 3.6 27.6 - - + -
353D GLY 3.2 4.7 - - - +
354D PHE* 4.2 22.9 - - + -
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Residues in contact with VAL 344 (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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149D LEU* 4.2 14.4 - - + -
150D PHE 4.0 4.9 - - - +
151D SER* 4.1 13.9 - - - -
179D ILE* 4.0 33.4 - - + -
188D LEU* 3.9 25.1 - - + -
190D TYR* 4.2 8.3 - - + +
342D TYR* 4.2 8.1 - - + -
343D VAL* 1.3 75.2 - - - +
345D PHE* 1.3 62.9 + - - +
346D ASP* 3.3 14.7 + - + +
352D ILE* 3.1 8.9 - - - +
353D GLY* 2.7 41.6 + - - +
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Residues in contact with PHE 345 (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* 3.7 16.2 - - + -
149D LEU* 3.4 14.9 - - - +
150D PHE* 2.8 50.8 + + + +
152D LEU* 3.9 12.1 - - + -
199D TYR* 3.7 47.6 - + + -
227D VAL* 3.5 34.1 - - + -
338D MET* 3.9 16.2 - - + -
343D VAL* 3.6 27.4 - - + -
344D VAL* 1.3 69.2 - - - +
346D ASP* 1.3 59.5 + - - +
347D ARG* 2.9 12.1 + - - +
351D ARG 3.9 2.2 - - - -
352D ILE* 4.2 10.5 - - + -
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Residues in contact with ASP 346 (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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149D LEU* 3.8 21.6 - - - +
190D TYR* 4.5 4.0 + - + -
193D ILE* 4.3 1.3 - - - +
344D VAL* 3.3 12.0 + - + +
345D PHE* 1.3 69.2 - - - +
347D ARG* 1.3 55.8 + - - +
348D ALA* 3.4 10.7 + - - +
349D ARG* 2.8 33.0 + - - +
350D LYS 2.9 7.6 + - - -
351D ARG* 2.9 78.7 + - + +
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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