Contacts of the helix formed by residues 586 - 600 (chain B) in PDB entry 6A5T
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 PRO 586 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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571B THR* 3.4 33.0 - - + +
573B ILE* 6.3 0.2 - - + -
583B HIS* 4.6 4.5 - - + +
584B ARG 3.6 9.4 - - - +
585B ASP* 1.3 92.0 - - - +
587B SER* 1.3 62.9 + - - +
588B MET 3.5 0.7 - - - -
589B LEU* 3.3 17.0 + - + +
590B VAL* 2.9 31.2 + - + +
610B ARG* 3.2 33.0 - - - +
617B PHE* 5.4 2.5 - - + -
61I ASP* 5.6 1.3 - - - +
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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
----------------------------------------------------------
585B ASP* 3.4 13.5 + - - -
586B PRO* 1.3 81.3 - - - +
588B MET* 1.3 65.9 + - - +
590B VAL* 3.1 5.6 + - - +
591B SER* 3.0 23.1 + - - -
610B ARG* 3.4 12.8 - - - +
61I ASP* 3.9 18.4 - - - -
64I GLN* 4.1 14.6 + - - -
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Residues in contact with MET 588 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554B TRP* 4.6 31.4 - - + +
583B HIS* 5.7 7.0 - - + +
585B ASP* 4.8 11.2 + - - +
586B PRO 3.5 0.2 - - - -
587B SER* 1.3 80.2 + - - +
589B LEU* 1.3 73.7 + - + +
591B SER* 3.5 6.4 - - - -
592B THR* 3.0 31.6 + - - +
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Residues in contact with LEU 589 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551B LEU* 4.3 14.8 - - + +
554B TRP* 4.0 30.7 - - + +
556B MET* 6.2 0.7 - - + -
573B ILE* 4.2 17.9 - - + -
583B HIS* 4.9 13.2 - - + +
585B ASP 4.7 3.0 + - - +
586B PRO* 3.3 21.0 + - + +
587B SER 3.1 0.6 - - - -
588B MET* 1.3 90.0 - - + +
590B VAL* 1.3 64.6 + - - +
592B THR* 3.2 3.3 + - - -
593B MET* 2.9 39.2 + - + +
617B PHE* 3.6 31.6 - - + -
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Residues in contact with VAL 590 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586B PRO* 2.9 16.6 + - + +
587B SER* 3.1 14.8 - - - +
589B LEU* 1.3 75.4 - - - +
591B SER* 1.3 62.9 + - - +
593B MET* 3.8 7.2 - - - +
594B ARG* 2.9 43.8 + - - +
608B ILE* 5.1 3.1 - - + +
610B ARG* 4.1 29.8 - - + +
617B PHE* 3.2 42.4 - - + -
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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
----------------------------------------------------------
587B SER* 3.0 13.8 + - - -
588B MET* 3.5 13.0 - - - -
590B VAL* 1.3 81.3 - - - +
592B THR* 1.3 65.6 + - - +
594B ARG* 3.2 9.3 + - - +
595B ASP* 3.0 29.9 + - - +
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Residues in contact with THR 592 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554B TRP* 4.6 23.6 - - + -
588B MET* 3.0 29.1 + - - +
589B LEU* 3.9 2.9 - - - -
591B SER* 1.3 76.3 + - - +
593B MET* 1.3 69.7 + - + +
595B ASP* 3.3 10.5 + - + +
596B LEU* 2.9 39.7 + - + +
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Residues in contact with MET 593 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547B ILE* 6.0 3.4 - - - -
550B PHE* 4.1 23.1 - - + +
551B LEU* 4.5 15.9 - - + -
554B TRP* 3.7 34.5 - - + +
589B LEU* 2.9 33.3 + - + +
590B VAL* 3.8 7.0 - - - +
591B SER 3.1 0.4 - - - -
592B THR* 1.3 81.0 - - + +
594B ARG* 1.3 63.5 + - - +
596B LEU* 3.2 17.6 + - + +
597B ARG* 2.9 19.6 + - - +
602B ILE* 4.2 14.7 - - - +
608B ILE* 3.4 27.4 - - + +
617B PHE* 5.0 4.7 - - + -
619B ILE* 5.2 3.1 - - + -
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Residues in contact with ARG 594 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
590B VAL* 2.9 36.4 + - - +
591B SER* 3.9 8.8 - - - +
593B MET* 1.3 73.4 - - - +
595B ASP* 1.3 68.0 + - - +
597B ARG* 3.2 21.9 + - - +
598B ARG* 3.0 57.4 + - - +
608B ILE* 4.0 21.6 + - + +
609B ILE* 5.9 0.2 - - - +
610B ARG* 5.1 12.9 - - - +
635B ASP* 5.2 6.6 + - - -
688B GLU* 4.6 1.8 - - - -
694B GLU* 3.9 18.3 + - - -
740B HIS* 5.8 2.9 - - - -
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Residues in contact with ASP 595 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
591B SER* 3.0 21.9 + - - +
592B THR* 3.5 15.8 + - + +
594B ARG* 1.3 76.0 - - - +
596B LEU* 1.3 61.7 + - + +
598B ARG* 2.8 26.0 + - - +
599B SER* 2.8 25.6 + - - -
646B ARG* 5.8 2.3 + - - -
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Residues in contact with LEU 596 (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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550B PHE* 4.7 17.0 - - + -
554B TRP* 5.6 2.9 - - + +
592B THR* 2.9 35.3 + - + +
593B MET* 3.8 14.8 - - + +
595B ASP* 1.3 73.3 - - + +
597B ARG* 1.3 62.6 + - - +
599B SER* 2.7 41.3 + - - +
600B GLY* 2.9 7.8 + - - -
601B ALA* 4.0 11.2 + - + -
602B ILE* 3.5 24.6 + - + +
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Residues in contact with ARG 597 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593B MET 2.9 14.0 + - - +
594B ARG* 3.6 20.5 + - - +
596B LEU* 1.3 75.2 - - - +
598B ARG* 1.3 61.1 + - - +
600B GLY* 3.8 7.4 + - - -
602B ILE* 4.0 16.1 - - + +
603B SER 4.0 13.5 - - - +
604B PRO* 4.5 18.0 + - + +
606B VAL* 3.2 36.9 + - + +
607B SER* 4.5 3.0 + - - +
608B ILE* 4.7 17.0 - - + +
682B VAL* 5.7 1.4 - - - +
683B THR* 6.1 0.2 - - - -
688B GLU* 3.7 34.1 + - + +
689B TYR* 2.6 33.5 + - - +
690B VAL* 5.1 0.6 - - - +
694B GLU* 3.4 28.7 + - - -
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Residues in contact with ARG 598 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
594B ARG* 3.0 41.1 + - + +
595B ASP* 2.8 22.7 + - - +
597B ARG* 1.3 80.1 - - + +
599B SER* 1.3 59.5 + - - +
600B GLY 3.3 0.2 - - - -
632B ILE* 3.5 38.0 - - + +
633B VAL 5.6 0.2 + - - -
635B ASP* 4.3 21.4 + - - -
646B ARG* 4.9 15.5 - - - +
682B VAL 3.9 12.1 - - - +
683B THR* 3.4 14.4 - - - +
684B SER 4.3 0.5 - - - -
685B GLY* 4.0 16.1 - - - -
687B ILE 5.8 0.4 - - - +
688B GLU* 2.2 55.1 + - + +
739B THR 5.0 1.2 + - - -
740B HIS* 4.3 7.3 + - - -
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Residues in contact with SER 599 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
595B ASP 2.8 10.5 + - - -
596B LEU* 2.7 46.6 + - - +
598B ARG* 1.3 73.2 - - - +
600B GLY* 1.3 55.5 + - - -
601B ALA* 3.5 8.4 + - - +
683B THR* 3.6 11.3 - - - +
684B SER 5.7 1.3 - - - -
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Residues in contact with GLY 600 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596B LEU 2.9 5.7 + - - -
597B ARG 4.3 4.3 - - - -
598B ARG 3.3 2.7 - - - -
599B SER* 1.3 78.5 - - - +
601B ALA* 1.3 60.0 + - - +
602B ILE 2.7 23.2 - - - +
604B PRO* 4.7 8.2 - - - +
683B THR* 4.8 18.2 - - - -
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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