Contacts of the helix formed by residues 581 - 593 (chain B) in PDB entry 5MKE
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 ARG 581 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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579B PHE 3.7 0.2 - - - -
580B ASN* 1.3 132.8 + - + +
582B THR* 1.3 62.5 + - + +
583B MET* 3.0 23.6 - - + +
584B SER* 2.7 25.7 + - - -
585B GLN* 3.3 5.8 + - - +
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Residues in contact with THR 582 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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581B ARG* 1.3 79.3 - - + +
583B MET* 1.3 67.3 + - - +
585B GLN* 3.0 10.1 + - - +
586B LEU* 3.0 43.7 + - - +
691B LEU* 6.2 4.0 - - + -
694B GLN* 3.9 24.0 - - - +
695B LYS* 6.1 2.5 - - - +
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Residues in contact with MET 583 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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578B ASN* 4.7 4.6 + - + -
580B ASN* 3.3 35.4 - - - +
581B ARG* 3.7 19.1 - - + -
582B THR* 1.3 83.0 + - - +
584B SER* 1.3 61.8 + - - +
586B LEU* 3.5 11.4 + - - +
587B SER* 3.7 10.0 + - - -
595C LYS* 6.4 1.6 - - - -
596C ASP* 6.2 0.2 - - - +
599C GLY* 4.0 30.5 - - - +
600C PHE* 4.1 19.1 - - + -
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Residues in contact with SER 584 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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578B ASN* 3.0 34.2 + - - +
579B PHE* 3.0 11.6 - - - -
580B ASN* 2.6 34.8 + - - -
581B ARG 2.7 16.0 + - - -
583B MET* 1.3 74.6 - - - +
585B GLN* 1.3 59.1 + - - -
586B LEU 3.6 0.2 + - - -
587B SER* 4.1 6.6 + - - -
588B THR* 3.7 12.3 + - - -
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Residues in contact with GLN 585 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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581B ARG 3.3 6.1 + - - +
582B THR* 3.0 12.8 + - - +
584B SER* 1.3 80.8 - - - +
586B LEU* 1.3 67.8 + - + +
588B THR* 3.3 29.8 + - - +
589B THR* 4.2 7.1 + - - +
694B GLN* 5.0 12.3 - - - +
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Residues in contact with LEU 586 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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582B THR* 3.0 31.8 + - - +
583B MET* 3.5 6.5 + - - +
584B SER 3.4 0.2 - - - -
585B GLN* 1.3 81.9 - - + +
587B SER* 1.3 62.6 + - - +
588B THR 3.1 2.5 - - - -
589B THR* 2.4 30.6 + - + +
590B MET* 3.4 3.7 + - - +
684B TYR* 5.8 4.7 - - + +
687B VAL* 4.4 19.0 - - + +
690B ASP* 5.9 1.3 - - - +
691B LEU* 3.5 50.0 - - + +
694B GLN* 6.2 0.9 - - - +
600C PHE* 4.6 13.9 - - + -
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Residues in contact with SER 587 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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574B PHE* 4.6 15.9 - - - -
578B ASN* 4.8 9.9 - - - -
583B MET 3.7 7.8 + - - -
584B SER 4.7 3.6 - - - -
585B GLN 3.5 0.4 - - - -
586B LEU* 1.3 74.9 - - - +
588B THR* 1.3 66.9 + - - +
590B MET* 2.9 34.2 + - - +
591B SER* 3.8 3.6 + - - -
1008B PLM 5.3 0.9 + - - -
600C PHE* 3.5 29.1 - - - -
603C MET* 5.2 0.5 - - - -
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Residues in contact with THR 588 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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507B TRP* 4.8 27.3 - - + +
584B SER 3.7 10.8 + - - -
585B GLN* 3.3 32.5 + - - +
586B LEU 3.1 0.2 - - - -
587B SER* 1.3 77.6 - - - +
589B THR* 1.3 65.5 + - + +
591B SER* 4.1 0.9 + - - -
592B ARG* 3.1 34.4 + - + +
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Residues in contact with THR 589 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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585B GLN* 4.6 9.4 - - - +
586B LEU* 2.4 25.6 + - + +
588B THR* 1.3 78.7 - - + +
590B MET* 1.3 56.1 + - - +
592B ARG* 2.7 15.8 + - + -
593B CYS* 2.5 39.9 + - - -
686B GLU* 6.0 0.4 - - - -
687B VAL* 3.3 25.9 - - + +
690B ASP* 3.9 21.5 - - - +
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Residues in contact with MET 590 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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586B LEU 3.4 1.7 + - - +
587B SER* 2.9 35.2 + - - +
589B THR* 1.3 81.6 + - - +
591B SER* 1.3 59.1 + - - +
593B CYS* 3.6 9.7 - - - -
594B ALA* 3.1 20.5 + - + +
687B VAL* 5.8 1.3 - - - -
1008B PLM 3.6 19.7 - - - +
600C PHE* 4.8 4.9 - - + -
603C MET* 4.0 22.2 - - + +
671C ILE* 3.5 38.6 - - + -
675C MET* 4.2 29.8 - - + +
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Residues in contact with SER 591 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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587B SER 3.8 4.3 + - - -
588B THR 5.2 0.9 - - - -
590B MET* 1.3 79.8 - - - +
592B ARG* 1.3 60.9 + - - +
593B CYS 3.2 0.4 - - - -
594B ALA* 2.7 31.5 + - - +
595B LYS* 3.4 5.5 + - - +
598B PHE* 5.6 5.4 - - - -
1008B PLM 5.1 14.8 - - - -
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Residues in contact with ARG 592 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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504B ARG* 4.9 26.2 - - - +
505B SER 4.5 8.7 + - - -
506B PHE* 5.7 4.6 - - - +
507B TRP* 4.0 21.8 - - - +
588B THR* 3.1 32.4 + - + +
589B THR* 2.7 19.4 + - + +
591B SER* 1.3 73.5 - - - +
593B CYS* 1.3 56.9 + - - +
595B LYS* 4.0 13.0 + - - +
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Residues in contact with CYS 593 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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589B THR* 2.5 41.6 + - - +
590B MET* 3.6 11.4 - - - -
592B ARG* 1.3 70.8 - - + +
594B ALA* 1.3 57.6 + - - +
595B LYS* 3.1 7.7 + - - +
596B ASP* 3.9 11.4 + - - +
679B ILE* 4.8 1.7 - - - +
683B THR* 3.2 54.6 + - + +
684B TYR* 4.9 0.7 - - - -
686B GLU* 5.1 4.3 - - - +
687B VAL* 4.7 4.3 - - - -
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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