Contacts of the helix formed by residues 587 - 596 (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 ASN 587 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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442S SER* 5.1 1.6 - - - -
585S GLU 4.1 0.2 + - - -
586S MET* 1.3 73.6 - - - +
588S ALA* 1.3 61.0 + - - +
589S ASP* 3.4 6.1 - - + +
590S GLN* 3.4 13.7 + - + +
591S LEU* 3.1 26.3 + - - +
64T TYR* 5.8 1.0 + - - -
106T GLY 4.2 13.8 + - - +
107T GLN* 4.1 10.3 + - - +
108T GLY* 2.8 37.9 + - - +
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Residues in contact with ALA 588 (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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442S SER* 3.2 31.7 + - - +
445S SER* 3.5 22.7 - - - -
446S GLY* 3.6 9.1 - - - +
587S ASN* 1.3 70.2 - - - +
589S ASP* 1.3 64.8 + - - +
591S LEU* 3.4 4.5 + - - +
592S TRP* 3.0 26.9 + - - +
298T LEU* 4.2 9.4 - - + -
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Residues in contact with ASP 589 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587S ASN* 3.4 4.5 - - + +
588S ALA* 1.3 76.7 - - - +
590S GLN* 1.3 60.8 + - + +
592S TRP* 3.7 9.0 + - - +
593S GLU* 3.4 22.2 + - - +
298T LEU* 3.6 30.0 - - + +
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Residues in contact with GLN 590 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543S PRO* 5.0 6.9 - - - +
586S MET* 3.7 34.0 - - + +
587S ASN* 3.4 12.7 + - + +
588S ALA 3.2 0.4 - - - -
589S ASP* 1.3 76.0 - - + +
591S LEU* 1.3 61.9 + - - +
592S TRP 3.3 0.2 - - - -
593S GLU* 3.4 4.3 + - - +
594S THR* 2.9 42.1 + - + +
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Residues in contact with LEU 591 (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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439S ALA 4.8 0.2 - - - +
442S SER* 3.8 16.6 - - - +
443S THR* 3.6 42.2 - - + +
446S GLY* 5.8 0.4 - - - -
506S MET* 4.9 3.4 - - + -
542S PRO* 5.6 0.2 - - + -
583S LEU* 3.8 39.3 - - + +
586S MET* 4.0 18.7 - - + +
587S ASN 3.1 16.5 + - - +
588S ALA* 3.6 5.4 - - - +
590S GLN* 1.3 74.7 - - - +
592S TRP* 1.3 63.7 + - - +
594S THR* 4.1 0.4 - - - -
595S THR* 3.3 40.5 + - + +
596S MET* 3.6 11.4 + - - +
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Residues in contact with TRP 592 (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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446S GLY* 3.2 32.1 - - - +
448S ASP* 3.6 25.1 - - + -
452S GLN* 3.4 21.8 - - - -
588S ALA 3.0 15.5 + - - +
589S ASP* 3.7 8.7 - - - +
591S LEU* 1.3 75.4 - - - +
593S GLU* 1.3 69.3 + - + +
596S MET* 3.1 33.5 + - + -
597S ASN* 2.8 67.2 + - + +
598S PRO* 4.1 7.4 - - + -
298T LEU* 6.2 0.7 - - + -
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Residues in contact with GLU 593 (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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589S ASP 3.4 15.1 + - - +
590S GLN* 3.4 6.0 + - - +
592S TRP* 1.3 89.2 - - + +
594S THR* 1.3 63.3 + - + +
597S ASN* 4.2 9.6 - - - +
600S HIS* 3.5 26.9 - - - +
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Residues in contact with THR 594 (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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541S GLN 4.9 5.2 - - - +
543S PRO* 3.6 31.8 - - + +
586S MET* 3.9 3.5 - - - +
590S GLN* 2.9 29.9 + - + +
591S LEU 3.7 1.2 + - - -
593S GLU* 1.3 81.5 - - + +
595S THR* 1.3 75.9 + - - +
600S HIS* 4.2 3.6 - - - +
601S ARG* 3.6 18.3 - - - -
602S ALA* 4.5 2.4 + - - +
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Residues in contact with THR 595 (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 4.3 - - - -
506S MET* 3.5 29.8 - - + -
540S ALA* 3.9 14.7 - - + +
541S GLN 4.5 3.6 - - - +
542S PRO* 3.8 18.2 - - + +
543S PRO* 3.8 12.8 - - - +
591S LEU* 3.3 23.5 + - + +
594S THR* 1.3 92.3 + - - +
596S MET* 1.3 60.1 + - - +
601S ARG* 3.4 19.2 - - - +
602S ALA 5.6 0.2 - - - +
603S LEU* 4.1 10.4 - - - +
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Residues in contact with MET 596 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432S PHE* 4.0 32.1 - - + -
443S THR* 3.6 44.9 - - + +
446S GLY* 4.5 3.4 - - - -
447S ARG* 3.6 30.1 - - + -
452S GLN* 2.8 32.3 + - - +
454S ILE* 4.7 0.4 - - + -
506S MET* 4.5 6.5 - - + -
591S LEU* 3.7 19.3 - - + +
592S TRP* 3.1 20.3 + - + +
595S THR* 1.3 80.8 - - - +
597S ASN* 1.3 61.5 + - - +
598S PRO* 3.3 2.1 - - - +
601S ARG* 3.1 14.1 + - - +
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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