Contacts of the helix formed by residues 436 - 447 (chain S) 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 S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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434S VAL* 3.4 1.7 - - - +
435S GLU* 1.3 82.8 - - - +
437S ASP* 1.3 57.2 + - - -
438S SER* 3.2 6.9 + - - -
439S ALA* 3.3 4.0 + - - +
440S GLY* 2.8 30.5 + - - -
456S PRO* 3.7 8.3 - - - +
457S LEU 3.4 9.6 - - - -
123T TYR* 5.6 0.2 - - - -
2009V G 3.8 4.7 - - - -
2010V G 3.0 12.3 - - - -
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Residues in contact with ASP 437 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417S LYS* 5.1 6.4 - - - +
436S GLY* 1.3 64.7 - - - -
438S SER* 1.3 63.5 + - - +
440S GLY* 3.7 4.9 - - - +
441S GLY* 3.0 19.3 + - - +
444S LYS* 5.4 2.2 + - - +
456S PRO* 3.9 17.7 - - - +
457S LEU 5.1 0.7 - - - +
109T ASN* 3.2 9.6 + - - -
119T ALA* 5.1 2.7 - - - -
2010V G 2.4 50.1 + - - +
2011V C 3.5 21.5 + - - -
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Residues in contact with SER 438 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435S GLU* 6.3 1.1 - - - -
436S GLY* 4.5 3.5 - - - -
437S ASP* 1.3 80.5 + - - +
439S ALA* 1.3 60.6 + - - +
442S SER* 3.5 7.1 + - - -
584S GLY 4.3 11.8 - - - -
109T ASN* 3.4 21.0 + - - +
119T ALA* 3.7 17.5 - - - +
123T TYR* 2.8 63.2 + - - -
2010V G 4.1 0.9 + - - -
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Residues in contact with ALA 439 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434S VAL* 4.0 12.8 - - + -
435S GLU* 3.7 17.5 - - + +
436S GLY 3.3 7.1 + - - +
438S SER* 1.3 76.3 - - - +
440S GLY* 1.3 63.2 + - - +
441S GLY 3.3 0.3 + - - -
442S SER* 3.3 6.3 + - - -
443S THR* 2.6 32.7 + - - -
583S LEU* 3.4 31.4 - - + -
584S GLY 4.5 7.6 - - - +
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Residues in contact with GLY 440 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434S VAL* 3.9 16.4 - - - +
436S GLY 2.8 21.5 + - - -
437S ASP* 3.7 4.0 - - - -
438S SER 3.4 0.6 - - - -
439S ALA* 1.3 71.9 - - - +
441S GLY* 1.3 55.1 + - - +
443S THR* 3.5 2.5 - - - -
444S LYS* 2.9 41.0 + - - +
454S ILE* 4.3 2.2 - - - +
456S PRO* 4.3 13.2 - - - -
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Residues in contact with GLY 441 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437S ASP* 3.0 11.5 + - - +
440S GLY* 1.3 71.5 - - - +
442S SER* 1.3 64.8 + - - +
444S LYS* 3.3 10.5 + - - +
445S SER* 3.1 26.0 + - - -
109T ASN* 3.4 21.5 - - - -
116T ASP* 4.5 13.1 - - - +
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Residues in contact with SER 442 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438S SER 3.5 13.8 + - - -
439S ALA 3.3 7.1 + - - -
441S GLY* 1.3 74.1 - - - +
443S THR* 1.3 58.4 + - - +
445S SER* 4.8 0.9 - - - -
446S GLY* 3.2 20.3 + - - -
583S LEU 4.5 4.9 - - - -
584S GLY 4.5 3.3 - - - -
586S MET 3.6 21.1 + - - -
587S ASN* 5.2 0.2 - - - -
588S ALA* 3.2 23.9 - - - +
591S LEU* 3.8 15.9 - - - +
108T GLY 4.3 0.7 - - - -
109T ASN* 3.5 20.8 + - - +
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Residues in contact with THR 443 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432S PHE* 4.6 1.3 - - + -
434S VAL* 4.0 6.0 - - + +
439S ALA* 2.6 25.1 + - - +
440S GLY* 3.5 6.1 - - - -
442S SER* 1.3 73.3 - - - +
444S LYS* 1.3 59.0 + - - +
446S GLY* 3.1 1.4 + - - -
447S ARG* 2.9 33.1 + - - +
454S ILE* 3.4 30.1 - - + -
506S MET* 3.7 22.9 - - + +
583S LEU* 4.8 0.2 - - - +
591S LEU* 3.6 16.6 - - - +
596S MET* 3.6 21.3 - - + +
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Residues in contact with LYS 444 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417S LYS* 3.6 10.2 + - - +
419S ALA* 3.6 30.2 - - + +
437S ASP* 5.4 2.4 + - - +
440S GLY* 2.9 26.4 + - - +
441S GLY* 3.3 9.5 + - - +
443S THR* 1.3 74.5 - - - +
445S SER* 1.3 58.8 + - - +
447S ARG* 3.1 25.6 + - - +
449S SER* 5.7 0.2 - - - -
454S ILE* 3.5 33.0 - - + -
456S PRO* 3.5 23.3 - - - +
116T ASP* 6.5 0.4 - - - -
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Residues in contact with SER 445 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441S GLY 3.1 12.2 + - - -
442S SER* 3.7 3.8 - - - -
443S THR 3.2 0.2 - - - -
444S LYS* 1.3 77.3 - - - +
446S GLY* 1.3 62.3 + - - +
447S ARG 3.5 4.3 + - - +
588S ALA* 3.5 19.7 - - - -
112T SER* 4.5 16.3 - - - -
297T SER* 5.0 2.6 - - - -
298T LEU* 4.4 21.3 + - - +
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Residues in contact with GLY 446 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442S SER 3.2 6.8 + - - -
443S THR* 3.1 6.8 + - - -
445S SER* 1.3 76.0 - - - +
447S ARG* 1.3 65.2 - - - +
588S ALA* 3.6 24.8 - - - +
591S LEU* 5.8 0.2 - - - -
592S TRP* 3.2 30.0 - - - +
596S MET* 4.5 5.6 - - - -
298T LEU* 5.3 7.7 - - - +
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Residues in contact with ARG 447 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419S ALA* 2.9 42.7 + - - +
420S ASP 3.3 18.4 + - - -
421S CYS 4.1 0.4 - - - +
443S THR 2.9 12.6 + - - +
444S LYS* 3.1 27.0 + - - +
445S SER 4.0 4.7 - - - +
446S GLY* 1.3 80.5 - - - +
448S ASP* 1.3 57.1 + - - +
449S SER* 3.6 32.3 + - - +
452S GLN* 2.8 51.2 + - + +
453S ALA* 3.9 0.4 - - - +
454S ILE* 3.5 13.4 - - + +
592S TRP* 4.2 1.8 - - - -
596S MET* 3.6 15.2 - - + -
296T THR 5.6 0.5 - - - +
297T SER* 5.0 11.4 - - - -
298T LEU 5.7 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