Contacts of the helix formed by residues 311 - 321 (chain A) in PDB entry 2VZE
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 ALA 311 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260A ILE 4.6 3.0 + - - -
265A TRP* 4.4 13.2 - - + -
310A GLY* 1.3 76.6 - - - -
312A PRO* 1.3 70.8 - - + +
313A ILE* 4.2 13.5 - - + -
314A VAL* 2.8 31.0 + - + +
315A TYR* 3.8 2.8 + - - -
337A VAL 3.2 12.5 + - - +
338A GLY* 5.1 0.9 - - - -
339A GLU* 5.3 0.2 - - + -
469A SER 4.9 1.6 - - - +
470A GLY* 4.2 25.8 - - - +
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Residues in contact with PRO 312 (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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311A ALA* 1.3 85.8 - - + +
313A ILE* 1.3 62.6 + - - +
315A TYR* 3.1 11.8 + - + +
316A ARG* 2.9 32.9 + - + +
336A THR* 3.1 19.2 - - + +
337A VAL 3.4 11.2 - - - +
339A GLU* 3.6 42.0 - - + +
340A SER 4.0 14.8 - - - +
341A LEU* 4.3 17.5 - - + +
342A LEU 5.7 0.2 - - - +
345A THR* 4.8 0.7 - - + +
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Residues in contact with ILE 313 (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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291A PHE* 5.0 7.6 - - + -
311A ALA* 3.0 17.1 + - + -
312A PRO* 1.3 79.6 - - - +
314A VAL* 1.3 65.9 + - + +
316A ARG* 3.3 14.8 + - + +
317A MET* 2.9 48.5 + - + +
339A GLU* 4.3 6.6 + - - +
469A SER* 4.0 33.0 - - - +
470A GLY 4.3 2.7 - - - +
500A VAL 4.7 2.2 - - - +
501A ARG* 3.9 43.1 - - + +
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Residues in contact with VAL 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A ILE* 4.1 34.1 - - + +
291A PHE* 4.0 26.0 - - + -
296A ILE* 4.3 12.3 - - + +
308A MET* 4.4 9.0 - - + -
310A GLY* 4.4 5.2 - - - -
311A ALA* 2.8 27.8 + - + +
313A ILE* 1.3 81.0 - - + +
315A TYR* 1.3 63.7 + - + +
317A MET* 3.3 9.9 + - - +
318A LEU* 3.1 35.3 + - + +
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Residues in contact with TYR 315 (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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308A MET* 3.5 31.5 - - + +
310A GLY* 3.8 14.3 + - - -
311A ALA 4.0 9.9 - - - -
312A PRO* 3.1 9.3 + - + +
314A VAL* 1.3 78.2 - - + +
316A ARG* 1.3 61.6 + - - +
318A LEU* 3.3 5.9 + - + +
319A LEU* 3.0 28.7 + - - +
334A CYS* 3.4 14.2 - - + +
335A VAL 2.9 40.3 + - - -
336A THR* 3.8 13.5 - - - -
341A LEU* 5.4 0.7 - - + -
345A THR* 4.1 7.9 - - + -
349A TRP* 3.8 43.0 - + + -
357A ILE* 3.7 27.1 - - + -
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Residues in contact with ARG 316 (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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312A PRO* 2.9 26.9 + - + +
313A ILE* 3.8 17.3 - - + +
315A TYR* 1.3 75.7 - - - +
317A MET* 1.3 63.4 + - - +
319A LEU* 3.4 15.5 + - + +
320A GLN* 3.5 18.5 + - - +
342A LEU* 3.6 29.0 - - - +
345A THR* 3.7 26.0 + - + +
498A ASP 4.9 0.4 + - - -
499A PRO 3.0 26.5 + - - -
500A VAL* 3.5 20.7 + - - +
501A ARG 3.8 2.2 + - - -
502A GLY* 3.5 24.7 - - - +
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Residues in contact with MET 317 (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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291A PHE* 3.6 41.7 - - + +
293A PRO* 3.3 46.5 - - + +
296A ILE* 4.9 4.7 - - + -
313A ILE* 2.9 38.0 + - + +
314A VAL* 3.7 5.8 - - - +
316A ARG* 1.3 76.2 - - + +
318A LEU* 1.3 66.0 + - + +
320A GLN* 3.2 16.8 + - - +
321A GLN* 3.6 14.7 + - - +
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Residues in contact with LEU 318 (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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293A PRO* 3.6 21.1 - - + +
296A ILE* 3.5 30.5 - - + -
297A LEU* 4.0 21.5 - - + +
300A LEU* 4.1 16.6 - - + -
308A MET* 4.4 5.2 - - + -
314A VAL* 3.1 29.7 + - + +
315A TYR* 3.3 6.9 + - - +
317A MET* 1.3 76.9 - - + +
319A LEU* 1.3 59.2 + - - +
321A GLN* 3.0 26.1 + - + +
323A LEU* 3.8 13.2 - - + +
349A TRP* 3.7 31.6 - - + -
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Residues in contact with LEU 319 (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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315A TYR 3.0 21.2 + - - +
316A ARG* 3.8 8.3 - - + +
317A MET 3.2 0.6 - - - -
318A LEU* 1.3 76.0 - - - +
320A GLN* 1.3 66.6 + - - +
321A GLN 3.6 6.7 + - - +
323A LEU* 4.2 11.3 - - + +
345A THR* 3.8 37.2 - - + +
348A ASN* 3.3 54.9 + - + +
349A TRP* 3.8 17.7 - - + +
352A GLN* 3.7 24.2 - - - +
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Residues in contact with GLN 320 (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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316A ARG 3.5 13.7 + - - +
317A MET* 3.2 11.6 + - - +
318A LEU 3.1 0.8 - - - -
319A LEU* 1.3 83.9 - - - +
321A GLN* 1.3 66.1 + - - +
348A ASN* 5.4 3.3 + - - -
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Residues in contact with GLN 321 (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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293A PRO* 3.7 35.8 - - + +
294A LEU* 3.5 37.5 - - - +
297A LEU* 4.2 15.9 - - + -
317A MET 3.6 13.7 - - - +
318A LEU* 3.0 15.9 + - - +
319A LEU 3.7 8.1 - - - +
320A GLN* 1.3 85.9 - - - +
322A ASP* 1.3 62.5 + - - +
323A LEU* 3.2 8.8 + - - +
352A GLN* 5.5 1.9 + - - -
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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