Contacts of the helix formed by residues 587 - 596 (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 ASN 587 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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442K SER* 5.3 0.4 - - - -
585K GLU 5.5 0.2 - - - -
586K MET* 1.3 76.5 - - - +
588K ALA* 1.3 59.8 - - - +
589K ASP* 3.1 21.7 + - - +
590K GLN* 3.4 12.2 + - + +
591K LEU* 3.1 26.1 + - - +
106L GLY 5.1 0.7 - - - +
107L GLN* 4.1 19.7 + - - +
108L GLY* 3.4 28.0 + - - +
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Residues in contact with ALA 588 (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 31.8 - - - +
445K SER* 3.5 22.0 - - - -
446K GLY* 3.6 8.9 - - - +
586K MET 4.2 0.4 + - - -
587K ASN* 1.3 70.1 - - - +
589K ASP* 1.3 64.1 + - - +
591K LEU* 3.4 4.5 + - - +
592K TRP* 3.0 25.6 + - - +
298L LEU* 3.7 11.9 - - + -
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Residues in contact with ASP 589 (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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587K ASN* 3.1 27.9 + - - +
588K ALA* 1.3 73.7 - - - +
590K GLN* 1.3 71.6 + - - +
592K TRP* 3.7 7.4 + - - +
593K GLU* 3.4 22.5 + - - +
298L LEU* 3.5 17.7 - - + +
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Residues in contact with GLN 590 (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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543K PRO* 5.0 6.9 - - - +
586K MET* 3.7 36.5 - - + +
587K ASN* 3.4 13.2 + - + +
588K ALA 3.3 0.4 - - - -
589K ASP* 1.3 84.2 + - - +
591K LEU* 1.3 62.9 + - - +
592K TRP 3.3 0.4 - - - -
593K GLU* 3.4 4.5 + - - +
594K THR* 2.9 42.2 + - + +
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Residues in contact with LEU 591 (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* 3.8 17.5 - - - +
443K THR* 3.6 41.7 - - - +
446K GLY* 5.8 0.4 - - - -
506K MET* 4.9 4.3 - - + -
583K LEU* 3.8 39.9 - - + +
586K MET* 3.9 19.6 - - + +
587K ASN 3.1 17.2 + - - +
588K ALA* 3.6 5.2 - - - +
590K GLN* 1.3 74.4 - - - +
592K TRP* 1.3 63.1 + - - +
594K THR* 4.1 0.7 - - - -
595K THR* 3.3 39.5 + - + +
596K MET* 3.6 12.2 + - - +
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Residues in contact with TRP 592 (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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446K GLY* 3.1 32.3 - - - +
447K ARG 4.2 0.2 - - - -
448K ASP* 3.6 23.1 - - + -
452K GLN* 3.4 23.8 - - - -
588K ALA 3.0 16.1 + - - +
589K ASP* 3.7 9.2 - - - +
591K LEU* 1.3 75.2 - - - +
593K GLU* 1.3 67.6 - - + +
596K MET* 3.1 33.5 + - + -
597K ASN* 2.8 67.6 + - + +
598K PRO* 4.1 7.4 - - + -
298L LEU* 5.2 2.0 - - + -
299L ARG* 4.1 29.1 - - - +
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Residues in contact with GLU 593 (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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589K ASP 3.4 15.2 + - - +
590K GLN* 3.4 6.7 + - - +
592K TRP* 1.3 88.7 - - + +
594K THR* 1.3 62.7 + - + +
597K ASN* 4.2 10.2 + - - +
600K HIS* 3.5 27.7 - - - +
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Residues in contact with THR 594 (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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541K GLN 5.0 4.9 - - - +
543K PRO* 3.6 30.5 - - + +
586K MET* 3.9 3.6 - - - +
590K GLN* 2.9 29.2 + - + +
591K LEU 3.8 1.0 + - - -
593K GLU* 1.3 81.7 - - + +
595K THR* 1.3 76.5 + - - +
600K HIS 4.3 3.2 - - - +
601K ARG* 3.6 17.7 - - - -
602K ALA* 4.4 3.3 + - - +
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Residues in contact with THR 595 (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* 4.6 4.0 - - - -
506K MET* 3.5 28.9 - - + -
540K ALA* 3.9 15.0 - - + +
541K GLN 4.5 2.9 - - - +
542K PRO* 3.8 20.3 - - + +
543K PRO* 3.8 12.1 - - - +
591K LEU* 3.3 21.2 + - + +
592K TRP 3.6 0.2 + - - -
594K THR* 1.3 92.5 + - - +
596K MET* 1.3 60.7 + - - +
601K ARG* 3.4 20.3 - - - +
602K ALA 5.6 0.9 - - - +
603K LEU* 4.1 10.2 - - - +
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Residues in contact with MET 596 (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* 4.0 33.2 - - + -
443K THR* 3.6 44.4 - - + +
446K GLY 4.5 3.6 - - - -
447K ARG* 3.6 30.3 - - + -
452K GLN* 2.8 33.9 + - - +
454K ILE* 4.7 0.7 - - + -
506K MET* 4.5 8.3 - - + -
591K LEU* 3.7 17.9 - - + +
592K TRP* 3.1 19.2 + - + +
595K THR* 1.3 82.7 - - - +
597K ASN* 1.3 62.9 + - - +
598K PRO* 3.3 1.7 - - - +
601K ARG* 3.1 13.9 + - - +
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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