Contacts of the helix formed by residues 436 - 447 (chain m) in PDB entry 6QX2
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 436 (chain m).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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434m VAL* 3.4 1.9 - - - +
435m GLU* 1.3 78.4 - - - +
437m ASP* 1.3 56.8 + - - -
438m SER 3.2 3.4 - - - -
439m ALA* 3.3 5.2 + - - +
440m GLY* 2.8 31.7 + - - -
456m PRO* 3.7 8.1 - - - +
457m LEU 3.4 11.0 - - - -
2009o G 3.9 21.5 + - - -
2010o G 4.0 0.4 - - - -
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Residues in contact with ASP 437 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109j ASN* 3.5 7.6 + - - -
119j ALA* 5.9 0.4 - - - -
417m LYS* 5.8 1.9 - - - +
436m GLY* 1.3 69.4 - - - -
438m SER* 1.3 65.6 + - - +
440m GLY* 3.7 5.4 - - - +
441m GLY* 3.0 19.6 + - - -
456m PRO* 3.9 17.1 - - - +
457m LEU 5.0 1.4 - - - +
458m ARG* 5.6 2.3 + - - +
2009o G 4.3 0.2 + - - -
2010o G 2.9 50.7 + - - +
2011o C 3.5 11.6 + - - -
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Residues in contact with SER 438 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109j ASN* 3.3 17.3 + - - +
119j ALA* 3.9 27.8 - - - +
123j TYR* 3.4 31.1 - - - -
436m GLY 4.7 0.2 - - - -
437m ASP* 1.3 77.9 + - - +
439m ALA* 1.3 59.3 + - - +
442m SER* 3.5 12.5 + - - -
584m GLY* 3.8 15.4 - - - -
2009o G 3.6 14.1 + - - -
2010o G 3.6 10.6 + - - -
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Residues in contact with ALA 439 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434m VAL* 4.0 20.2 - - + -
435m GLU* 4.5 8.7 - - + +
436m GLY 3.3 8.9 + - - +
438m SER* 1.3 76.4 - - - +
440m GLY* 1.3 63.3 + - - +
441m GLY 3.3 0.2 + - - -
442m SER* 3.3 2.3 + - - -
443m THR* 2.6 33.7 + - - +
583m LEU* 4.1 27.8 - - + +
584m GLY* 3.9 10.7 - - - +
2009o G 5.8 1.3 - - - +
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Residues in contact with GLY 440 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434m VAL* 3.9 15.4 - - - +
436m GLY 2.8 20.1 + - - -
437m ASP* 3.7 4.5 - - - -
438m SER 3.4 0.4 - - - -
439m ALA* 1.3 72.6 - - - +
441m GLY* 1.3 55.4 + - - +
443m THR* 3.5 2.1 - - - -
444m LYS* 2.9 39.6 + - - +
454m ILE* 4.3 5.5 - - - +
456m PRO* 4.3 11.2 - - - -
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Residues in contact with GLY 441 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109j ASN* 3.7 18.8 - - - -
116j ASP* 5.7 11.0 - - - -
437m ASP* 3.0 12.2 + - - +
440m GLY* 1.3 70.6 - - - +
442m SER* 1.3 64.7 + - - +
444m LYS* 3.3 10.0 + - - +
445m SER* 3.1 27.0 + - - -
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Residues in contact with SER 442 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108j GLY 4.4 0.2 - - - -
109j ASN* 3.4 27.1 + - - +
438m SER 3.5 6.2 + - - -
439m ALA 3.3 8.6 + - - -
441m GLY* 1.3 73.5 - - - +
443m THR* 1.3 56.3 + - - +
445m SER* 4.8 1.1 - - - -
446m GLY* 3.2 21.1 + - - -
583m LEU 3.7 18.1 + - - -
584m GLY 4.3 0.2 + - - -
586m MET 3.6 17.2 + - - -
587m ASN* 5.5 0.2 - - - -
588m ALA* 3.2 24.2 - - - +
591m LEU* 3.8 11.6 - - - +
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Residues in contact with THR 443 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432m PHE* 4.6 1.1 - - + -
434m VAL* 4.0 5.6 - - + +
439m ALA* 2.6 26.7 + - - +
440m GLY* 3.5 6.3 - - - -
442m SER* 1.3 73.8 - - - +
444m LYS* 1.3 58.4 + - - +
446m GLY* 3.1 1.7 + - - -
447m ARG* 2.9 32.7 + - - +
454m ILE* 3.4 28.9 - - + -
506m MET* 3.7 22.9 - - + +
583m LEU* 5.5 0.2 - - - +
591m LEU* 3.6 16.7 - - - +
596m MET* 3.6 21.1 - - + +
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Residues in contact with LYS 444 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116j ASP* 5.3 9.2 - - - +
419m ALA* 3.9 27.8 - - + -
440m GLY* 2.9 25.5 + - - +
441m GLY* 3.3 8.5 + - - +
443m THR* 1.3 75.6 - - - +
445m SER* 1.3 58.4 + - - +
447m ARG* 3.1 25.9 + - - +
454m ILE* 3.5 24.9 - - + -
456m PRO* 5.6 5.2 - - + -
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Residues in contact with SER 445 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112j SER* 4.6 15.8 - - - -
297j SER* 4.6 2.9 - - - -
298j LEU* 3.5 42.2 + - - +
441m GLY 3.1 12.4 + - - -
442m SER* 3.7 4.0 - - - -
444m LYS* 1.3 77.9 - - - +
446m GLY* 1.3 61.0 + - - +
447m ARG 3.5 3.6 + - - +
588m ALA* 3.6 19.7 - - - -
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Residues in contact with GLY 446 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298j LEU* 5.1 3.3 + - - +
442m SER 3.2 7.8 + - - -
443m THR 3.1 5.4 + - - -
445m SER* 1.3 79.4 - - - +
447m ARG* 1.3 63.3 + - - +
588m ALA* 3.6 25.5 - - - +
591m LEU* 5.8 0.7 - - - -
592m TRP* 3.2 30.1 - - - +
596m MET* 4.5 5.6 - - - -
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Residues in contact with ARG 447 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297j SER* 4.5 12.8 - - - -
419m ALA* 2.9 43.7 + - - +
420m ASP 3.3 17.8 + - - -
421m CYS 4.1 0.2 - - - +
443m THR 2.9 14.5 + - - +
444m LYS* 3.1 27.7 + - - +
445m SER 3.4 4.9 - - - +
446m GLY* 1.3 80.4 - - - +
448m ASP* 1.3 58.1 + - - +
449m SER* 3.6 32.7 + - - +
452m GLN* 2.8 51.1 + - + +
453m ALA* 3.9 0.6 - - - +
454m ILE* 3.5 13.4 - - + +
592m TRP* 4.2 1.6 - - - -
596m MET* 3.6 15.2 - - + -
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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