Contacts of the helix formed by residues 337 - 344 (chain A) in PDB entry 2VGB
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 337 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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335A VAL* 3.0 20.3 + - + +
336A ALA* 1.3 71.8 - - - +
338A GLY* 1.3 55.4 + - - +
340A LEU* 4.0 7.0 - - - -
341A GLY* 2.5 33.1 + - - -
349A VAL* 3.8 21.7 - - + +
353A GLN* 3.0 24.2 + - - +
369A CYS* 3.8 9.2 - - - -
370A ALA 2.6 31.3 + - - +
371A THR 3.0 20.4 + - - -
373A MET* 3.6 10.9 - - - +
390A ASP* 2.6 46.0 + - - -
581A PGA 3.4 2.2 + - - -
385C ARG* 3.1 42.3 + - + +
389C SER* 3.9 5.5 - - - -
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Residues in contact with GLY 338 (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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221A ASP* 6.1 0.7 - - - -
337A ARG* 1.3 79.2 - - - +
339A ASP* 1.3 60.1 + - - -
341A GLY 3.3 3.6 + - - -
342A ILE* 3.3 9.3 - - - +
371A THR* 3.6 16.3 - - - +
581A PGA 2.9 17.5 + - - -
385C ARG* 2.8 33.0 + - - -
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Residues in contact with ASP 339 (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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253A ASN* 3.3 19.5 + - - +
287A PHE* 3.3 26.2 - - + -
315A GLU* 2.4 26.3 - - + +
338A GLY* 1.3 68.8 - - - +
340A LEU* 1.3 59.4 + - - +
342A ILE* 2.7 31.0 + - - +
343A GLU* 2.9 17.0 + - + +
581A PGA 3.0 11.9 + - - +
583A MN 1.9 37.5 + - - -
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Residues in contact with LEU 340 (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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314A ILE 4.1 8.5 - - - +
315A GLU 3.2 6.8 + - - +
316A ASN* 3.6 28.3 - - - +
320A VAL* 3.6 20.9 - - + -
335A VAL* 4.6 7.2 - - + -
336A ALA 3.1 18.7 + - - +
337A ARG* 3.6 4.0 - - - +
339A ASP* 1.3 77.9 - - - +
341A GLY* 1.3 56.7 + - - +
343A GLU* 4.5 0.7 - - - -
344A ILE* 3.0 51.9 + - + +
349A VAL* 4.1 15.5 - - + -
352A ALA* 3.8 26.0 - - + -
356A MET* 4.1 15.7 - - + -
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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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337A ARG 2.5 21.9 + - - -
338A GLY 3.7 1.6 - - - -
339A ASP 3.0 0.6 + - - -
340A LEU* 1.3 72.8 - - - +
342A ILE* 1.3 60.9 + - - +
344A ILE 3.4 9.6 - - - +
346A ALA* 4.0 16.7 + - - +
349A VAL* 3.5 19.1 - - - -
382C ARG* 4.9 6.1 + - - -
385C ARG* 3.9 12.2 + - - -
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Residues in contact with ILE 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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218A TYR* 3.7 33.4 - - + -
221A ASP* 3.5 35.2 - - - +
222A GLY* 3.6 5.2 - - - +
253A ASN* 3.5 41.7 - - + +
255A PRO* 3.1 24.1 - - - +
338A GLY 3.3 20.4 - - - +
339A ASP* 2.7 12.1 + - - +
341A GLY* 1.3 76.0 - - - +
343A GLU* 1.3 63.6 - - - +
344A ILE 3.4 4.0 - - - +
382C ARG* 6.0 0.7 - - - +
385C ARG* 3.8 7.4 - - - +
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Residues in contact with GLU 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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253A ASN* 3.2 30.3 - - - +
254A LEU 4.0 18.3 + - - +
255A PRO* 3.2 27.0 - - - +
256A GLY 4.6 2.1 + - - -
257A ALA 5.5 0.9 - - - +
259A VAL* 5.7 4.7 - - - +
287A PHE* 5.3 6.7 - - + -
315A GLU 3.3 24.9 - - - +
316A ASN* 3.8 25.0 + - + +
317A HIS* 4.6 6.0 - - + +
339A ASP* 2.9 15.8 + - + +
340A LEU* 4.1 1.6 - - - +
342A ILE* 1.3 78.3 - - - +
344A ILE* 1.3 61.3 + - + +
345A PRO* 4.9 0.2 - - - +
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Residues in contact with ILE 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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255A PRO* 6.0 0.2 - - - -
317A HIS* 4.0 29.4 - - + +
340A LEU* 3.0 39.6 + - + +
341A GLY 3.4 15.1 - - - +
342A ILE 3.8 3.2 - - - -
343A GLU* 1.3 80.7 - - - +
345A PRO* 1.3 80.2 - - + +
346A ALA 3.3 2.1 + - - -
348A LYS* 4.0 14.6 - - + -
349A VAL* 3.8 27.4 - - + +
352A ALA* 4.7 1.3 - - + -
78C ILE* 4.0 35.4 - - + -
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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