Contacts of the helix formed by residues 327 - 332 (chain A) in PDB entry 2VZ3
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 GLY 327 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324A ASP* 2.8 16.6 + - - +
325A LYS 3.2 2.0 + - - -
326A GLN* 1.3 76.9 - - - +
328A LEU* 1.3 67.2 + - - -
329A TYR 3.1 2.9 - - - -
330A ARG* 3.1 7.3 + - - +
331A SER* 3.0 24.5 + - - -
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Residues in contact with LEU 328 (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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289A SER* 3.3 17.3 - - - +
294A VAL* 3.6 12.5 - - + +
295A PHE* 3.3 41.5 - - - +
296A GLU* 3.7 12.8 - - + +
317A VAL* 5.6 0.2 - - + -
321A LEU* 3.6 41.7 - - + -
326A GLN 3.9 0.6 + - - -
327A GLY* 1.3 71.6 - - - -
329A TYR* 1.3 63.2 + - - +
330A ARG 3.1 0.9 + - - -
331A SER* 3.3 15.0 + - - +
332A ASP* 3.6 14.0 - - + +
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Residues in contact with TYR 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A SER* 3.4 26.3 - - - -
290A TRP* 3.1 53.3 + + - -
294A VAL* 3.6 21.8 - - + +
326A GLN* 3.9 28.5 - - + +
328A LEU* 1.3 77.6 - - - +
330A ARG* 1.3 94.8 + - + +
333A ASN* 3.1 18.2 + - - +
1640A ACT 4.7 2.8 + - - -
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Residues in contact with ARG 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A TYR* 3.7 16.6 - - - -
290A TRP* 3.9 3.4 - - - -
324A ASP* 3.5 22.4 - - - +
326A GLN* 2.9 37.7 + - + +
327A GLY 3.1 3.7 + - - +
329A TYR* 1.3 102.0 - - + +
331A SER* 1.3 61.1 + - - +
332A ASP 3.1 2.9 - - - -
333A ASN* 3.0 33.4 + - - +
382A MET* 3.3 8.9 - - - +
405A TYR* 3.6 37.1 - - + -
406A GLN* 2.7 27.1 + - - -
463A PRO* 5.3 0.6 - - - +
1640A ACT 2.9 39.2 + - - -
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Residues in contact with SER 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A MET* 4.0 3.1 - - - +
321A LEU* 3.5 12.9 - - - +
322A THR* 3.1 61.3 + - - +
324A ASP* 4.0 5.6 - - - -
327A GLY* 3.0 13.5 + - - -
328A LEU* 3.3 28.3 + - - +
330A ARG* 1.3 78.4 - - - +
332A ASP* 1.3 57.6 + - - +
333A ASN 3.4 1.4 + - - +
350A PRO* 5.7 0.3 - - - +
382A MET* 4.5 1.4 - - - +
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Residues in contact with ASP 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A TYR 4.7 0.3 - - - +
273A GLN* 4.9 0.5 - - - -
274A SER 5.6 0.2 + - - -
286A ILE 4.4 1.9 - - - +
287A GLY* 3.7 15.4 - - - -
288A GLY 3.2 21.2 + - - -
289A SER* 2.6 44.9 + - - -
295A PHE 4.3 4.0 - - - +
297A LYS* 4.7 3.3 + - - +
317A VAL* 4.0 5.2 - - + -
320A MET* 3.6 18.9 - - - +
321A LEU* 3.6 21.3 - - + -
328A LEU* 3.6 11.3 - - + +
331A SER* 1.3 77.5 + - - +
333A ASN* 1.3 72.2 + - - +
334A HIS 4.0 0.5 + - - -
335A ALA 4.9 0.5 + - - -
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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