Contacts of the strand formed by residues 339 - 345 (chain A) in PDB entry 3VG1
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 ARG 339 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178A TYR* 3.5 48.1 + - + -
179A THR 3.4 16.2 - - - +
180A PRO* 4.4 0.9 - - + -
181A ILE* 3.7 5.4 - - - +
278A GLU* 2.8 40.6 + - - +
334A ASP* 2.9 57.7 + - + +
337A ARG* 3.4 54.1 - - - +
338A LYS* 1.3 79.4 - - - +
340A ILE* 1.3 66.1 + - - +
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Residues in contact with ILE 340 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177A TRP 3.8 0.7 - - - +
178A TYR* 3.3 3.0 - - - -
179A THR* 2.9 41.0 + - + +
181A ILE* 3.9 14.8 - - + -
187A TYR* 3.7 29.6 - - + -
189A VAL* 3.8 22.2 - - + -
215A VAL* 3.9 9.9 - - + -
331A VAL* 3.8 18.6 - - + -
332A VAL 3.1 10.8 - - - +
333A PHE* 4.2 13.9 - - + -
339A ARG* 1.3 79.9 - - - +
341A GLY* 1.3 61.4 + - - +
342A PHE* 3.6 24.7 - - + -
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Residues in contact with GLY 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A LEU* 3.8 10.1 - - - -
177A TRP 3.1 9.4 - - - -
178A TYR* 3.4 21.5 - - - -
330A TYR 3.5 0.2 - - - +
331A VAL* 3.2 8.0 - - - +
332A VAL* 2.8 36.1 + - - -
340A ILE* 1.3 73.9 - - - +
342A PHE* 1.3 63.9 + - - -
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Residues in contact with PHE 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A SER 3.7 0.2 - - - +
176A LEU* 3.5 3.6 - - - +
177A TRP 2.7 33.1 + - - +
179A THR* 4.2 5.2 - - + -
215A VAL* 4.5 12.8 - - + -
275A LEU* 3.6 22.2 - - + -
284A PHE* 4.0 25.4 - + + -
286A ILE* 4.2 25.8 - - + -
321A MET* 4.1 20.0 - - + -
325A ILE* 5.3 4.5 - - + -
326A MET* 5.5 2.7 - - + -
329A PHE* 4.6 10.8 - + + -
330A TYR 3.5 2.7 - - - -
331A VAL* 4.1 26.9 - - + -
340A ILE* 3.6 30.3 - - + -
341A GLY* 1.3 74.4 - - - -
343A ALA* 1.3 61.3 + - - +
358A VAL* 3.6 14.5 - - + +
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Residues in contact with ALA 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A TYR* 3.4 37.2 - - + -
173A THR 4.3 0.7 - - - +
175A SER 3.5 15.5 - - - +
176A LEU* 3.6 12.6 - - + -
329A PHE* 3.3 7.3 - - - +
330A TYR 2.7 34.0 + - - +
342A PHE* 1.3 75.0 - - - +
344A VAL* 1.3 59.3 + - - +
358A VAL* 3.8 9.4 - - - -
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Residues in contact with VAL 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A TYR* 3.1 4.6 - - - +
173A THR* 2.9 47.8 + - - +
174A GLY* 6.2 0.4 - - - -
175A SER 4.9 0.6 + - - -
328A GLY 4.1 2.5 - - - -
329A PHE* 4.3 4.5 - - + -
343A ALA* 1.3 71.5 - - - +
345A SER* 1.3 59.3 + - - +
348A HIS* 3.3 46.7 - - + +
356A ALA 4.2 3.4 - - - +
357A ALA* 4.0 11.4 - - - +
358A VAL* 3.8 29.1 - - + +
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Residues in contact with SER 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A GLN* 3.9 12.3 - - - -
171A LEU 3.2 15.9 - - - -
172A TYR* 4.0 1.1 - - - +
173A THR* 4.9 2.6 + - - -
328A GLY 2.8 30.9 + - - -
329A PHE 3.6 2.9 - - - -
330A TYR 3.6 16.8 - - - +
343A ALA 3.3 1.6 + - - -
344A VAL* 1.3 76.4 - - - +
346A ALA* 1.3 63.8 + - - +
347A CYS* 3.2 20.6 + - - -
348A HIS* 3.1 23.2 + - - -
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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