Contacts of the helix formed by residues 585 - 596 (chain B) in PDB entry 5MJ6
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 GLN 585 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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478B LYS* 3.7 37.1 - - + +
481B ASN* 6.2 0.9 - - - +
482B ASP* 3.4 12.8 - - - +
485B LEU* 3.6 9.0 - - - +
575B TYR* 5.5 0.2 + - - -
584B ILE* 1.3 78.6 - - - +
586B SER* 1.3 68.9 + - - +
587B ASP* 3.2 8.0 - - + +
588B ASP* 2.7 32.3 + - - +
589B LEU 3.8 2.1 + - - -
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Residues in contact with SER 586 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482B ASP* 2.8 30.6 + - - -
484B TRP* 3.3 21.0 + - - -
485B LEU* 3.7 11.3 - - - +
531B SER* 3.8 9.8 + - - -
585B GLN* 1.3 72.9 - - - +
587B ASP* 1.3 64.8 + - - +
588B ASP 3.3 0.9 + - - -
589B LEU* 3.3 14.2 + - - +
590B TRP* 3.4 27.2 + - - -
611B THR* 5.0 5.9 - - - -
612B LEU* 6.5 0.4 - - - -
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Residues in contact with ASP 587 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
585B GLN* 3.1 7.1 + - + +
586B SER* 1.3 79.8 - - - +
588B ASP* 1.3 63.7 + - - +
590B TRP* 3.5 10.7 + - - +
591B ASP* 3.0 31.6 + - - +
604B LYS* 4.1 32.7 - - - +
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Residues in contact with ASP 588 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575B TYR* 4.1 3.2 - - - -
579B HIS* 4.0 20.2 - - + +
583B SER 4.3 1.7 - - - +
584B ILE* 3.2 23.6 - - + -
585B GLN* 2.7 40.3 + - - +
587B ASP* 1.3 78.6 - - - +
589B LEU* 1.3 61.5 + - - +
591B ASP* 3.3 20.5 - - - +
592B SER* 3.3 12.8 + - - -
1N NAG 3.3 20.6 + - - -
2N NAG 5.4 2.3 + - - +
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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
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484B TRP* 4.0 10.3 - - + -
485B LEU* 3.9 23.3 - - + -
489B PHE* 3.6 39.0 - - + -
556B LEU* 4.5 3.6 - - + -
571B ALA 6.4 0.4 - - - -
572B VAL* 6.0 1.6 - - + -
575B TYR* 3.6 36.0 - - + +
585B GLN 3.8 1.6 + - - +
586B SER 3.3 8.6 + - - +
587B ASP 3.2 0.8 - - - -
588B ASP* 1.3 76.5 - - - +
590B TRP* 1.3 90.1 - - + +
592B SER* 3.0 15.7 + - - -
593B PHE* 3.2 24.0 + - + -
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Residues in contact with TRP 590 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484B TRP* 3.5 35.9 - + - -
555B LEU* 5.1 0.9 - - + -
556B LEU* 4.9 5.2 - - + -
559B LEU* 3.5 25.6 - - + -
586B SER* 3.4 28.0 + - - -
587B ASP* 3.5 15.3 + - - +
589B LEU* 1.3 90.5 - - + +
591B ASP* 1.3 62.3 + - - +
593B PHE* 3.2 9.5 + + - +
594B ASN* 3.0 28.5 + - - +
603B VAL* 3.8 8.8 - - + +
604B LYS* 3.7 35.0 - - + +
607B MET* 3.3 47.2 + - + +
608B LYS* 5.8 0.6 - - - +
611B THR* 3.7 22.1 + - + +
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Residues in contact with ASP 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 ASP* 3.0 26.2 + - - +
588B ASP* 3.3 12.4 - - - +
590B TRP* 1.3 76.7 - - - +
592B SER* 1.3 61.5 + - - +
594B ASN* 3.3 16.9 + - - +
595B GLU* 3.4 23.5 + - - +
604B LYS* 2.9 29.1 + - - -
1N NAG 2.9 25.9 + - - +
2N NAG 3.8 27.9 + - - +
3N BMA 5.2 0.3 - - - -
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Residues in contact with SER 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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571B ALA* 3.9 23.0 - - - +
574B LEU* 4.3 9.5 - - - +
575B TYR* 3.5 28.3 + - - +
578B ASN* 5.5 0.9 + - - -
579B HIS* 4.5 5.7 - - - -
588B ASP 3.3 10.3 + - - -
589B LEU* 3.0 10.9 + - - -
591B ASP* 1.3 75.2 - - - +
593B PHE* 1.3 67.1 + - - +
594B ASN 3.3 0.2 + - - -
595B GLU* 3.3 20.1 + - - +
596B VAL* 3.5 19.4 + - - +
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Residues in contact with PHE 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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489B PHE* 5.2 1.3 - + - -
556B LEU* 5.2 3.4 - - + -
559B LEU* 3.9 20.0 - - + -
563B LEU* 3.7 26.7 - - + -
567B VAL* 5.1 2.9 - - + -
568B PHE* 3.7 44.4 - + - -
571B ALA* 3.7 28.9 - - + -
572B VAL* 5.2 2.7 - - + -
589B LEU* 3.2 39.9 + - + -
590B TRP* 3.2 18.2 + + - +
592B SER* 1.3 79.1 - - - +
594B ASN* 1.3 54.5 + - - +
596B VAL* 3.5 1.9 + - - +
597B THR* 2.5 37.1 + - - +
603B VAL* 3.8 20.9 - - + -
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Residues in contact with ASN 594 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
590B TRP 3.0 19.1 + - - +
591B ASP* 3.6 9.4 + - - +
592B SER 3.1 0.4 - - - -
593B PHE* 1.3 77.0 - - - +
595B GLU* 1.3 58.0 + - + +
597B THR* 2.7 27.3 + - - +
601B LEU 3.6 5.5 - - - +
602B ASP* 3.1 28.4 + - - -
603B VAL* 3.0 23.5 + - - +
604B LYS* 3.9 16.8 - - - +
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Residues in contact with GLU 595 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574B LEU* 3.7 27.0 - - + +
578B ASN* 4.8 0.5 + - - -
591B ASP* 3.4 18.4 + - - +
592B SER* 3.3 9.9 + - - +
593B PHE 3.3 0.6 - - - -
594B ASN* 1.3 79.2 - - + +
596B VAL* 1.3 59.3 + - - +
597B THR 3.2 3.7 + - - +
1N NAG 3.0 47.5 + - - +
2N NAG 6.4 1.6 - - - -
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Residues in contact with VAL 596 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567B VAL* 3.7 29.4 - - + +
570B HIS* 3.2 44.2 - - + +
571B ALA* 3.8 19.5 - - + +
574B LEU* 3.7 23.3 - - + -
592B SER 3.6 15.0 - - - +
593B PHE 3.5 4.7 + - - +
594B ASN 3.3 0.2 - - - -
595B GLU* 1.3 75.0 - - - +
597B THR* 1.3 64.4 + - - +
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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