Contacts of the helix formed by residues 591 - 605 (chain B) in PDB entry 5AIM
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 ASP 591 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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589B THR 3.4 4.0 + - - -
590B LEU* 1.3 72.3 - - - +
592B LYS* 1.3 83.5 + - - +
593B LYS* 3.3 21.8 + - - +
594B THR* 3.1 30.8 + - - +
595B VAL* 3.2 12.3 + - - +
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Residues in contact with LYS 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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574B GLU* 3.5 46.4 + - - +
577B TYR* 3.4 43.0 - - + +
589B THR* 4.8 10.9 - - - +
590B LEU 4.0 5.4 - - - +
591B ASP* 1.3 79.1 + - - +
593B LYS* 1.3 55.5 + - - +
595B VAL* 3.3 3.2 + - - +
596B ARG* 2.8 31.7 + - - +
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Residues in contact with LYS 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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591B ASP* 3.3 17.2 + - - +
592B LYS* 1.3 78.1 - - - +
594B THR* 1.3 61.2 + - - +
596B ARG* 3.3 7.1 + - + +
597B GLY* 2.8 27.7 + - - -
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Residues in contact with THR 594 (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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555B ARG* 3.3 44.7 + - - +
590B LEU* 5.5 3.8 - - + -
591B ASP* 3.1 30.5 + - - +
592B LYS 3.1 0.2 - - - -
593B LYS* 1.3 85.7 - - - +
595B VAL* 1.3 63.2 + - + +
597B GLY* 3.3 7.6 + - - -
598B ASP* 3.5 13.7 + - - +
1641B GOL 3.9 27.4 + - - +
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Residues in contact with VAL 595 (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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555B ARG* 4.9 6.3 - - - +
559B ILE* 4.1 22.2 - - + +
576B PHE* 4.7 1.6 - - + -
577B TYR* 3.9 31.2 - - + +
580B VAL* 4.6 13.5 - - + -
590B LEU* 3.6 36.8 - - + +
591B ASP 3.2 14.2 + - - +
592B LYS 3.9 4.0 - - - +
594B THR* 1.3 77.2 - - - +
596B ARG* 1.3 57.9 + - - +
598B ASP* 3.2 7.9 + - - +
599B VAL* 2.9 31.9 + - + +
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Residues in contact with ARG 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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572B LEU* 3.7 36.0 - - - +
577B TYR* 4.5 18.2 + - - +
592B LYS 2.8 18.4 + - - +
593B LYS* 3.6 9.4 - - + +
595B VAL* 1.3 75.3 - - - +
597B GLY* 1.3 59.5 + - - +
599B VAL* 3.2 7.5 + - - -
600B ASP* 2.8 60.8 + - - +
619B LYS* 4.3 19.8 - - - +
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Residues in contact with GLY 597 (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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593B LYS 2.8 18.5 + - - -
594B THR 3.3 3.5 + - - -
596B ARG* 1.3 73.0 - - - +
598B ASP* 1.3 57.9 + - - +
600B ASP* 3.2 10.6 + - - +
601B LEU* 2.9 31.9 + - - +
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Residues in contact with ASP 598 (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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552B SER* 2.6 35.4 + - - -
555B ARG* 2.7 46.1 + - + +
556B GLN* 3.9 11.3 + - + +
559B ILE* 4.2 9.9 - - + -
594B THR 3.5 4.4 + - - +
595B VAL 3.2 8.3 + - - +
597B GLY* 1.3 73.8 - - - +
599B VAL* 1.3 68.3 + - - +
600B ASP 3.1 0.2 - - - -
601B LEU* 3.2 14.5 + - - +
602B MET* 2.9 31.0 + - - +
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Residues in contact with VAL 599 (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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559B ILE* 3.8 18.1 - - + +
572B LEU* 4.0 26.2 - - + -
576B PHE* 4.5 7.4 - - + -
577B TYR* 5.7 0.4 - - + -
595B VAL* 2.9 26.1 + - + +
596B ARG* 3.5 11.0 - - - +
598B ASP* 1.3 75.7 - - - +
600B ASP* 1.3 60.5 + - - +
602B MET* 3.1 10.6 + - - +
603B VAL* 2.8 35.0 + - + +
608B LEU* 4.3 4.3 - - + -
621B ILE* 3.9 31.4 - - + -
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Residues in contact with ASP 600 (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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596B ARG* 2.8 51.7 + - - +
597B GLY* 3.4 11.2 - - - +
598B ASP 3.1 0.2 - - - -
599B VAL* 1.3 80.8 - - - +
601B LEU* 1.3 57.8 + - + +
603B VAL* 3.8 7.7 - - - +
604B GLU* 2.9 39.5 + - + +
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Residues in contact with LEU 601 (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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552B SER* 3.9 9.6 - - - +
556B GLN* 4.0 15.3 - - - +
597B GLY 2.9 17.5 + - - +
598B ASP* 3.2 28.0 + - - +
600B ASP* 1.3 77.2 - - + +
602B MET* 1.3 58.0 + - - +
604B GLU* 3.4 6.8 + - + +
605B SER* 3.0 30.9 + - - -
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Residues in contact with MET 602 (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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556B GLN* 3.4 55.9 - - + +
559B ILE* 3.7 29.6 - - + -
560B LEU* 3.5 31.2 - - + -
598B ASP 2.9 19.5 + - - +
599B VAL 3.5 6.1 - - - +
601B LEU* 1.3 74.3 - - - +
603B VAL* 1.3 63.6 + - - +
605B SER* 3.4 6.8 + - - -
606B GLU 3.0 3.5 + - - -
607B LYS* 2.9 38.5 + - + -
608B LEU* 3.3 21.0 + - + -
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Residues in contact with VAL 603 (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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599B VAL* 2.8 34.7 + - + +
600B ASP* 3.8 8.5 - - - +
602B MET* 1.3 72.0 - - - +
604B GLU* 1.3 73.6 + - - +
606B GLU* 3.1 16.1 + - - +
608B LEU* 3.6 27.1 - - + +
610B ALA* 3.7 35.4 - - + +
621B ILE* 4.6 1.6 - - + -
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Residues in contact with GLU 604 (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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600B ASP* 2.9 24.9 + - + +
601B LEU* 3.9 7.6 - - + +
602B MET 3.3 0.2 - - - -
603B VAL* 1.3 86.7 - - - +
605B SER* 1.3 57.0 + - - +
606B GLU* 3.3 8.1 + - - +
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Residues in contact with SER 605 (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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556B GLN* 5.3 0.9 + - - -
601B LEU 3.0 18.6 + - - -
602B MET* 3.4 6.6 + - - -
603B VAL 3.3 0.2 - - - -
604B GLU* 1.3 74.6 - - - +
606B GLU* 1.3 70.8 + - - +
607B LYS* 3.3 33.5 + - - +
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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