Contacts of the helix formed by residues 456 - 463 (chain D) in PDB entry 4QGC
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 ASN 456 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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433D LYS* 3.5 15.4 + - + +
434D SER* 5.6 0.8 - - - +
454D THR* 2.9 16.0 + - - +
455D ARG* 1.3 76.7 - - - +
457D PRO* 1.3 69.6 - - - +
458D GLN* 3.0 28.1 + - - +
459D THR* 3.3 29.6 + - + +
460D ALA 3.3 5.0 + - - -
473D LEU* 4.1 1.6 - - - -
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Residues in contact with PRO 457 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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455D ARG 3.2 11.4 - - - +
456D ASN* 1.3 87.8 - - - +
458D GLN* 1.3 61.3 + - + +
460D ALA* 3.5 4.7 - - + +
461D ARG* 3.2 45.7 + - - +
473D LEU* 3.8 26.0 - - + +
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Residues in contact with GLN 458 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236D ASP* 3.9 19.4 + - - -
237D VAL 4.1 12.5 + - - -
238D ASP* 3.7 10.8 + - - +
264D ASN* 3.3 34.6 + - - +
265D ILE* 4.8 3.8 - - - +
456D ASN* 3.0 12.6 + - - +
457D PRO* 1.3 76.2 - - - +
459D THR* 1.3 62.8 + - + +
460D ALA 3.1 1.1 - - - -
461D ARG* 3.1 17.2 + - - +
462D GLN* 2.8 57.6 + - - +
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Residues in contact with THR 459 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432D THR* 5.2 0.7 - - - +
433D LYS 3.2 21.5 + - - +
434D SER* 3.3 31.9 - - - +
435D GLY* 4.5 5.1 + - - -
439D HIS* 5.6 1.0 + - - -
454D THR* 3.3 19.6 + - - +
456D ASN* 3.3 25.1 + - - +
458D GLN* 1.3 74.2 - - + +
460D ALA* 1.3 62.4 + - - +
462D GLN* 3.8 12.5 - - - +
463D ALA* 3.0 30.0 + - - +
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Residues in contact with ALA 460 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107D PRO* 3.7 18.5 - - + +
454D THR* 3.8 15.9 - - + -
456D ASN 3.3 9.9 + - - +
457D PRO* 3.5 13.5 - - + +
458D GLN 3.1 0.2 - - - -
459D THR* 1.3 83.6 + - - +
461D ARG* 1.3 61.5 + - - +
463D ALA 3.7 1.7 + - - -
464D HIS* 4.2 0.5 - - - -
471D PRO* 3.1 37.6 - - + +
472D VAL 4.8 1.8 - - - +
473D LEU* 4.4 14.8 - - + -
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Residues in contact with ARG 461 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92D ARG* 5.7 4.0 - - - +
105D TYR* 5.9 1.9 + - - +
107D PRO* 4.1 15.5 - - + -
108D VAL 3.2 27.6 - - - +
109D ALA* 3.3 22.2 - - - +
110D VAL* 6.0 0.4 - - - -
236D ASP* 4.0 22.4 + - - -
238D ASP* 2.7 42.0 + - - +
239D MET* 4.6 0.3 - - - +
457D PRO* 3.2 37.5 + - - +
458D GLN* 3.1 23.2 + - - +
460D ALA* 1.3 77.5 - - - +
462D GLN* 1.3 62.8 + - - +
463D ALA 3.3 0.7 + - - -
464D HIS* 3.4 18.1 + - - +
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Residues in contact with GLN 462 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238D ASP* 2.9 36.6 + - + +
239D MET* 4.4 10.5 - - + -
264D ASN 2.9 26.1 + - - +
266D LYS* 3.3 37.9 + - + +
434D SER 5.1 1.6 - - - +
439D HIS* 5.4 1.8 - - - +
458D GLN* 2.8 38.3 + - - +
459D THR* 3.5 12.6 + - - +
460D ALA 3.4 0.2 - - - -
461D ARG* 1.3 71.8 - - - +
463D ALA* 1.3 63.7 + - - +
464D HIS 3.1 4.2 + - - -
465D LEU* 3.3 22.6 + - + +
466D TYR* 4.2 7.6 - - - -
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Residues in contact with ALA 463 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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435D GLY* 6.4 0.9 - - - -
438D ALA* 6.3 0.7 - - + -
439D HIS* 4.8 6.7 - - - +
452D ALA* 5.2 4.3 - - + -
459D THR 3.0 17.9 + - - +
461D ARG 3.2 0.8 - - - -
462D GLN* 1.3 73.8 - - - +
464D HIS* 1.3 61.8 + - - +
465D LEU 3.1 6.2 + - - -
466D TYR* 3.2 28.5 + - - +
469D ILE* 3.7 24.3 - - + +
471D PRO* 3.7 27.4 - - + -
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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