Contacts of the helix formed by residues 436 - 447 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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434K VAL* 3.4 1.9 - - - +
435K GLU* 1.3 87.2 - - - +
437K ASP* 1.3 57.7 + - - -
438K SER* 3.2 6.1 - - - -
439K ALA* 3.3 3.0 + - - +
440K GLY* 2.8 30.7 + - - -
456K PRO* 3.7 8.1 - - - +
457K LEU 3.4 11.0 - - - -
2009N G 4.0 6.3 - - - -
2010N G 3.8 8.3 - - - -
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Residues in contact with ASP 437 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417K LYS* 5.0 9.1 - - - +
436K GLY* 1.3 69.1 - - - -
438K SER* 1.3 64.0 + - - +
440K GLY* 4.1 4.5 - - - +
441K GLY* 3.0 19.5 + - - +
444K LYS* 6.2 1.1 - - - -
456K PRO* 3.9 18.1 - - - +
457K LEU 5.0 1.2 - - - +
458K ARG* 6.0 0.3 - - - +
109L ASN* 3.3 8.2 + - - -
119L ALA* 5.3 2.0 - - - -
2010N G 2.8 31.7 + - - +
2011N C 4.0 17.4 + - - -
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Residues in contact with SER 438 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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435K GLU* 4.4 3.9 + - - -
436K GLY* 4.5 2.6 - - - -
437K ASP* 1.3 79.6 + - - +
439K ALA* 1.3 59.3 + - - +
442K SER* 3.5 13.0 + - - -
584K GLY* 4.2 11.6 - - - +
109L ASN* 3.3 15.4 + - - +
119L ALA* 3.7 17.5 - - - +
120L ALA 5.2 0.2 + - - -
123L TYR* 2.6 59.5 + - - -
2010N G 3.9 6.5 + - - -
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Residues in contact with ALA 439 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434K VAL* 4.0 12.8 - - + -
435K GLU* 3.4 19.5 - - - +
436K GLY 3.3 5.4 + - - +
438K SER* 1.3 76.2 - - - +
440K GLY* 1.3 63.1 + - - +
441K GLY 3.3 0.3 + - - -
442K SER* 3.3 5.1 + - - -
443K THR* 2.6 33.0 + - - -
583K LEU* 3.4 33.2 - - + -
584K GLY* 4.1 8.2 - - - -
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Residues in contact with GLY 440 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434K VAL* 3.9 16.0 - - - +
436K GLY 2.8 21.6 + - - -
437K ASP* 3.4 5.1 + - - -
439K ALA* 1.3 71.8 - - - +
441K GLY* 1.3 55.2 + - - +
443K THR* 3.5 2.1 - - - -
444K LYS* 2.9 40.0 + - - +
454K ILE* 4.3 3.1 - - - +
456K PRO* 4.2 13.2 - - - -
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Residues in contact with GLY 441 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437K ASP 3.0 11.5 + - - -
440K GLY* 1.3 71.5 - - - +
442K SER* 1.3 65.0 - - - +
444K LYS* 3.3 10.7 + - - +
445K SER* 3.1 26.3 + - - -
109L ASN* 3.3 21.8 - - - -
116L ASP* 4.4 14.0 - - - +
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Residues in contact with SER 442 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438K SER 3.5 7.1 + - - -
439K ALA 3.3 7.8 + - - -
441K GLY* 1.3 75.2 - - - +
443K THR* 1.3 56.4 + - - +
445K SER* 4.8 0.9 - - - -
446K GLY 3.2 20.6 + - - -
583K LEU 4.2 8.1 + - - -
584K GLY 4.2 2.3 + - - -
586K MET 3.6 20.5 + - - -
588K ALA* 3.2 23.5 - - - +
591K LEU* 3.8 16.9 - - - +
108L GLY 4.6 0.3 - - - -
109L ASN* 3.5 26.4 + - - +
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Residues in contact with THR 443 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432K PHE* 4.7 1.1 - - + -
434K VAL* 4.0 6.0 - - + +
439K ALA* 2.6 25.3 + - - +
440K GLY* 3.5 5.8 - - - -
442K SER* 1.3 74.5 - - - +
444K LYS* 1.3 58.4 + - - +
446K GLY* 3.1 1.9 + - - -
447K ARG* 2.9 32.7 + - - +
454K ILE* 3.4 30.1 - - + -
506K MET* 3.7 23.1 - - + +
583K LEU* 5.2 0.3 - - - +
591K LEU* 3.6 16.6 - - - +
596K MET* 3.6 20.9 - - + +
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Residues in contact with LYS 444 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417K LYS* 3.4 24.4 + - - +
418K LEU 4.9 0.2 - - - -
419K ALA* 3.6 28.8 - - + +
437K ASP* 6.2 0.6 - - - -
440K GLY 2.9 26.3 + - - +
441K GLY* 3.3 8.9 + - - +
443K THR* 1.3 75.2 - - - +
445K SER* 1.3 58.7 + - - +
447K ARG* 3.1 25.3 + - - +
449K SER* 5.7 0.2 - - - -
454K ILE* 3.5 33.0 - - + -
456K PRO* 3.8 11.6 - - - +
116L ASP* 6.2 4.3 - - + +
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Residues in contact with SER 445 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441K GLY 3.1 13.0 + - - -
442K SER* 3.7 3.8 - - - -
443K THR 3.2 0.2 - - - -
444K LYS* 1.3 78.4 - - - +
446K GLY* 1.3 62.1 + - - +
447K ARG 3.5 4.7 + - - +
588K ALA* 3.5 20.9 - - - -
111L GLY 5.5 0.9 + - - -
112L SER* 4.5 17.0 - - - -
297L SER* 4.9 3.5 - - - -
298L LEU* 3.5 28.9 + - - +
299L ARG* 4.5 0.5 + - - -
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Residues in contact with GLY 446 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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442K SER 3.2 7.0 + - - -
443K THR 3.1 6.5 + - - -
445K SER* 1.3 77.7 - - - +
447K ARG* 1.3 56.2 + - - +
588K ALA* 3.6 25.1 - - - +
591K LEU* 5.8 0.4 - - - -
592K TRP* 3.1 20.3 - - - +
596K MET* 4.5 5.4 - - - -
298L LEU* 4.0 4.3 - - - -
299L ARG* 2.8 24.8 + - - -
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Residues in contact with ARG 447 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419K ALA* 2.9 43.3 + - - +
420K ASP 3.3 17.2 + - - -
421K CYS 4.1 0.4 - - - +
443K THR 2.9 14.1 + - - +
444K LYS* 3.1 25.7 + - - +
445K SER 3.4 4.0 - - - +
446K GLY* 1.3 81.9 - - - +
448K ASP* 1.3 57.0 + - - +
449K SER* 3.6 32.3 + - - +
452K GLN* 2.8 52.0 + - + +
453K ALA* 3.9 0.8 - - - +
454K ILE* 3.5 12.8 - - + +
592K TRP* 4.2 0.9 - - - -
596K MET* 3.6 15.7 - - + -
297L SER* 5.1 4.9 - - - -
299L ARG* 3.6 9.1 + - - -
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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