Contacts of the helix formed by residues 312 - 319 (chain A) in PDB entry 4ZGA
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 ASP 312 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172A ASP* 2.5 46.2 + - - +
173A GLY* 4.2 3.4 - - - -
309A GLU 3.4 5.1 + - - +
310A GLN 3.3 2.4 - - - -
311A PRO* 1.3 72.4 - - - +
313A PHE* 1.3 68.7 + - - +
314A SER 3.2 0.2 + - - -
315A GLY 3.4 0.2 + - - -
316A HIS* 2.8 39.5 + - - -
360A HIS* 3.2 6.9 - - - -
362A MET* 3.6 8.6 - - - +
475A HIS* 3.0 6.9 + - - -
903A ZN 2.2 36.3 - - - -
905A EDO 3.3 9.0 - - - -
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Residues in contact with PHE 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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309A GLU* 3.1 26.8 + - + +
310A GLN* 3.8 15.3 - - - +
311A PRO 3.4 0.8 - - - -
312A ASP* 1.3 84.9 - - - +
314A SER* 1.3 71.9 + - - +
316A HIS* 3.5 18.0 - - - +
317A LYS* 3.8 9.8 + - + +
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Residues in contact with SER 314 (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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310A GLN* 3.8 16.5 + - - -
311A PRO 3.4 2.9 + - - -
312A ASP 3.3 0.4 - - - -
313A PHE* 1.3 84.2 - - - +
315A GLY* 1.3 61.6 + - - +
317A LYS* 3.0 7.2 + - - +
318A TYR* 2.9 41.0 + - - -
325A MET* 3.4 20.9 - - - +
328A PRO* 3.9 22.3 - - - +
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Residues in contact with GLY 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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178A TYR* 4.8 2.2 - - - -
311A PRO 3.1 14.4 + - - -
312A ASP 3.8 3.1 - - - -
314A SER* 1.3 75.4 - - - +
316A HIS* 1.3 55.5 + - - +
319A GLY* 2.6 34.0 + - - -
325A MET* 3.6 19.1 - - - +
362A MET* 3.9 20.0 - - - -
473A GLY* 3.5 4.7 - - - -
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Residues in contact with HIS 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 ASP* 2.8 31.5 + - - -
313A PHE* 3.5 11.7 - + - +
314A SER 3.2 0.2 - - - -
315A GLY* 1.3 74.4 - - - +
317A LYS* 1.3 53.2 + - + +
362A MET* 3.8 3.1 - - + +
471A PHE* 3.2 14.9 - - + +
472A GLN 2.7 30.0 + - - -
473A GLY 3.2 20.0 + - - +
474A ASP* 3.6 13.1 + - - -
475A HIS* 3.4 17.7 - + - -
903A ZN 2.3 35.8 - - - -
905A EDO 3.1 9.4 + - - -
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Residues in contact with LYS 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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313A PHE* 4.4 9.4 - - + +
314A SER* 3.0 13.1 + - - +
316A HIS* 1.3 79.3 - - - +
318A TYR* 1.3 81.0 - - + +
470A PHE 4.1 15.0 - - - +
471A PHE* 4.5 0.4 - - - +
472A GLN* 3.5 21.9 + - - +
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Residues in contact with TYR 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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314A SER* 2.9 26.7 + - - +
317A LYS* 1.3 91.7 - - + +
319A GLY* 1.3 65.2 + - - +
322A GLY* 3.8 10.1 + - - -
324A GLU* 3.7 48.7 - - + +
325A MET* 3.4 28.7 - - + -
328A PRO* 5.9 0.4 - - + -
364A ASP* 5.5 0.2 - - - +
472A GLN* 4.0 14.3 - - - +
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Residues in contact with GLY 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 GLY* 2.6 27.8 + - - -
317A LYS 3.8 0.6 - - - -
318A TYR* 1.3 73.3 - - - +
320A PRO* 1.3 68.5 - - - +
321A PHE 3.3 1.8 - - - -
322A GLY* 2.7 27.3 + - - -
325A MET* 3.9 5.0 - - - +
364A ASP* 4.5 3.8 - - - -
472A GLN* 3.8 17.3 - - - +
473A GLY 4.0 0.2 - - - -
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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