Contacts of the helix formed by residues 580 - 595 (chain J) in PDB entry 6OD3
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 580 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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604I PRO 4.8 0.7 - - - -
605I GLN* 3.6 51.7 + - - +
608I LEU* 3.9 24.9 - - - +
578J ARG* 3.4 63.0 + - + +
579J LEU* 1.3 79.1 - - - +
581J VAL* 1.3 60.8 + - - +
582J ARG 3.2 2.7 - - - -
583J ASP* 3.8 20.5 + - + +
584J ILE* 2.8 36.1 + - + +
9Y T 5.6 3.2 + - - -
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Residues in contact with VAL 581 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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579J LEU* 3.8 30.1 - - + +
580J ARG* 1.3 76.2 - - - +
582J ARG* 1.3 58.0 + - - +
584J ILE* 4.0 4.9 - - - +
585J ASN* 3.0 53.9 + - - +
607J LYS* 5.5 4.7 - - - +
9Y T 6.3 6.0 - - - -
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Residues in contact with ARG 582 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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570F ARG* 5.9 2.8 - - - +
578J ARG* 4.6 12.1 - - - +
580J ARG 3.2 0.6 - - - -
581J VAL* 1.3 80.6 - - - +
583J ASP* 1.3 84.3 + - - +
585J ASN* 3.9 5.8 - - - +
586J GLU* 3.0 28.6 + - + +
10Y G 3.7 28.1 + - - +
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Residues in contact with ASP 583 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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608I LEU* 3.3 30.8 - - + +
612I HIS* 4.9 1.4 + - + +
578J ARG* 4.1 18.2 + - - -
580J ARG* 3.3 20.5 + - + +
582J ARG* 1.3 101.8 + - - +
584J ILE* 1.3 61.5 + - - +
586J GLU* 3.4 7.6 + - - +
587J ALA* 2.9 23.2 + - - +
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Residues in contact with ILE 584 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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588I PHE* 5.3 2.0 - - + -
604I PRO* 3.9 21.3 - - + +
607I LYS* 4.1 16.2 - - + -
608I LEU* 4.0 25.8 - - + +
611I LEU* 3.9 6.1 - - + -
579J LEU 3.5 22.4 - - - +
580J ARG* 2.8 21.2 + - + +
581J VAL* 4.0 4.7 - - - +
583J ASP* 1.3 71.3 - - - +
585J ASN* 1.3 59.6 + - - +
587J ALA* 3.1 2.5 + - - +
588J PHE* 2.7 60.3 + - + -
607J LYS* 4.9 4.7 - - - +
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Residues in contact with ASN 585 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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581J VAL* 3.0 40.3 + - - +
582J ARG* 3.9 6.0 - - - +
584J ILE* 1.3 76.1 - - - +
586J GLU* 1.3 58.8 + - - +
588J PHE* 3.4 7.4 + - - +
589J LYS* 3.0 27.9 + - - +
607J LYS* 3.1 33.7 + - - +
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Residues in contact with GLU 586 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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582J ARG* 3.0 19.8 + - + +
583J ASP* 3.7 9.0 - - - +
585J ASN* 1.3 76.1 - - - +
587J ALA* 1.3 61.2 + - - +
589J LYS* 3.5 7.4 + - - +
590J GLU* 3.2 23.0 + - - +
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Residues in contact with ALA 587 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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608I LEU* 3.7 13.9 - - + -
611I LEU* 3.6 29.3 - - + +
612I HIS* 3.8 15.9 - - + +
615I VAL* 4.9 1.7 - - - +
583J ASP 2.9 18.1 + - - +
584J ILE 3.1 4.5 + - - +
586J GLU* 1.3 75.5 - - - +
588J PHE* 1.3 59.5 + - - +
590J GLU* 3.4 6.2 + - - +
591J LEU* 3.0 29.6 + - - +
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Residues in contact with PHE 588 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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588I PHE* 3.5 32.1 - + - -
611I LEU* 3.5 25.8 - - + -
584J ILE* 2.7 43.4 + - + +
585J ASN* 3.7 7.4 - - - +
587J ALA* 1.3 73.8 - - - +
589J LYS* 1.3 53.0 + - - +
591J LEU* 3.8 2.6 - - - +
592J GLY 2.7 30.5 + - - -
607J LYS* 3.5 61.5 - - + -
610J ILE* 3.5 37.7 - - + +
611J LEU* 4.0 7.9 - - + -
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Residues in contact with LYS 589 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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585J ASN 3.0 16.3 + - - +
586J GLU* 3.7 8.3 - - - +
587J ALA 3.3 0.2 - - - -
588J PHE* 1.3 75.7 - - - +
590J GLU* 1.3 60.2 + - - +
592J GLY* 3.9 1.6 - - - -
593J ARG* 3.0 30.2 + - + +
610J ILE* 5.4 1.1 - - - -
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Residues in contact with GLU 590 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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615I VAL* 4.2 22.2 - - + -
586J GLU 3.2 16.5 + - - +
587J ALA* 3.8 7.0 - - - +
588J PHE 3.3 0.2 - - - -
589J LYS* 1.3 76.4 - - - +
591J LEU* 1.3 59.6 + - - +
593J ARG* 3.0 39.3 + - - +
594J MET* 3.1 32.7 + - + +
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Residues in contact with LEU 591 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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591I LEU* 4.4 4.3 - - + -
611I LEU* 3.7 27.6 - - + +
614I ALA* 3.9 23.1 - - + -
615I VAL* 3.7 24.6 - - + +
618I ILE* 4.0 16.4 - - + -
587J ALA 3.0 17.9 + - - +
588J PHE* 3.9 3.4 - - - +
590J GLU* 1.3 75.0 - - - +
592J GLY* 1.3 63.8 + - - +
594J MET* 3.2 11.1 + - + +
595J VAL* 3.3 13.8 + - + +
610J ILE* 3.8 20.2 - - + +
611J LEU* 5.0 0.9 - - + -
614J ALA* 3.8 26.0 - - + -
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Residues in contact with GLY 592 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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588J PHE 2.7 21.7 + - - -
589J LYS* 3.9 1.6 - - - -
591J LEU* 1.3 73.7 - - - +
593J ARG* 1.3 58.1 + - - +
595J VAL* 3.3 5.6 - - - +
596J GLN* 3.2 13.9 - - - +
605J GLN* 3.1 30.6 + - - +
610J ILE* 3.8 23.4 - - - +
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Residues in contact with ARG 593 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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589J LYS* 3.0 21.7 + - + +
590J GLU* 3.0 42.7 + - - +
591J LEU 3.2 0.2 - - - -
592J GLY* 1.3 75.7 - - - +
594J MET* 1.3 76.2 + - - +
595J VAL 3.4 0.2 - - - -
596J GLN* 3.4 33.1 + - - +
597J LEU* 4.4 1.6 + - - +
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Residues in contact with MET 594 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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615I VAL* 3.8 26.0 - - + +
618I ILE* 3.7 37.9 - - + -
619I LEU* 3.6 37.9 - - + -
622I GLU* 4.0 11.1 - - - +
590J GLU* 3.1 20.7 + - + +
591J LEU* 3.2 9.8 + - + +
593J ARG* 1.3 92.1 - - + +
595J VAL* 1.3 60.9 + - - +
596J GLN 3.2 1.0 + - - -
597J LEU* 3.5 13.2 + - - +
598J HIS* 3.9 13.3 + - - -
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Residues in contact with VAL 595 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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618I ILE* 4.2 11.2 - - + -
591J LEU* 3.3 13.7 + - + +
592J GLY* 3.3 19.5 - - - +
594J MET* 1.3 74.5 - - - +
596J GLN* 1.3 59.2 + - - +
597J LEU 3.2 0.7 - - - -
598J HIS* 3.2 4.9 + - - +
599J LEU* 3.0 31.4 + - + +
605J GLN* 3.4 4.0 - - - +
610J ILE* 5.1 1.6 - - + +
613J GLN* 3.3 32.3 - - + +
614J ALA* 4.0 26.5 - - + +
617J VAL* 3.9 27.4 - - + -
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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