Contacts of the helix formed by residues 588 - 603 (chain B) in PDB entry 4RG7
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 GLU 588 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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583B PHE* 2.9 16.7 + - + +
584B SER* 5.1 0.9 - - - -
586B GLN* 3.3 6.7 - - + +
587B ARG* 1.3 76.5 - - - +
589B HIS* 1.3 58.9 + - - +
590B ASP* 3.3 3.1 - - + +
591B ILE* 3.7 20.9 - - + +
592B ALA* 2.9 27.6 + - - +
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Residues in contact with HIS 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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584B SER* 5.7 1.3 - - - +
587B ARG 3.7 4.6 + - - -
588B GLU* 1.3 73.0 - - - +
590B ASP* 1.3 62.5 + - - +
592B ALA* 3.2 7.7 + - - +
593B ILE* 2.9 38.0 + - + +
616B GLU* 5.1 6.1 - - + +
619B LEU* 6.3 0.4 - - + -
620B THR* 3.6 31.0 - - + -
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Residues in contact with ASP 590 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588B GLU* 5.1 0.9 - - + -
589B HIS* 1.3 79.0 - - - +
591B ILE* 1.3 64.5 + - - +
593B ILE* 3.2 14.3 - - + +
594B LYS* 3.1 22.9 + - - +
620B THR* 5.6 1.7 - - - +
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Residues in contact with ILE 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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583B PHE* 4.2 13.2 - - + +
588B GLU* 3.3 24.7 + - + +
590B ASP* 1.3 78.0 - - - +
592B ALA* 1.3 62.5 + - - +
594B LYS* 3.4 17.8 - - - +
595B PHE* 3.4 10.6 + - - +
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Residues in contact with ALA 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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580B GLY* 3.7 25.7 - - - +
583B PHE* 4.2 4.4 - - - +
584B SER* 4.0 17.0 - - - +
588B GLU 2.9 14.0 + - - +
589B HIS* 3.3 13.0 - - - +
591B ILE* 1.3 77.2 - - - +
593B ILE* 1.3 62.5 + - + +
595B PHE* 3.2 6.6 + - - +
596B PHE* 3.1 21.2 + - - +
616B GLU* 5.0 10.5 - - + -
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Residues in contact with ILE 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 HIS* 2.9 16.7 + - + +
590B ASP* 3.2 22.2 - - - +
592B ALA* 1.3 72.5 - - - +
594B LYS* 1.3 71.0 + - + +
596B PHE* 4.0 7.7 - - - +
597B GLN* 3.1 46.2 + - - +
613B LEU* 5.2 7.2 - - + +
616B GLU* 4.2 27.4 - - + +
617B PHE* 5.3 2.5 - - + +
620B THR* 6.0 1.8 - - + +
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Residues in contact with LYS 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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590B ASP 3.1 14.4 + - - +
591B ILE* 3.4 15.9 - - - +
592B ALA 3.2 0.2 - - - -
593B ILE* 1.3 84.7 - - + +
595B PHE* 1.3 60.1 + - - +
597B GLN* 3.7 7.7 + - - +
598B ARG* 3.4 17.8 + - - +
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Residues in contact with PHE 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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576B TRP* 3.7 22.9 - - + +
579B ALA* 4.3 8.5 - - + +
580B GLY* 3.7 23.1 - - - +
591B ILE 3.4 7.4 + - - +
592B ALA 3.2 8.4 + - - +
593B ILE 3.2 0.4 - - - -
594B LYS* 1.3 78.3 - - - +
596B PHE* 1.3 66.2 + - - +
597B GLN 3.2 0.2 - - - -
598B ARG* 3.0 10.3 + - - +
599B ALA 2.9 18.7 + - - -
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Residues in contact with PHE 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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576B TRP 4.5 3.1 + - - -
577B CYS* 5.7 2.2 - - - +
580B GLY* 4.7 3.5 - - - -
592B ALA 3.1 15.5 + - - +
593B ILE* 4.0 6.3 - - - +
595B PHE* 1.3 76.0 - - - +
597B GLN* 1.3 58.1 + - + +
599B ALA* 3.3 10.2 + - - +
600B ILE* 3.1 24.8 + - - +
609B ALA* 4.0 13.6 - - + +
612B LEU* 5.0 4.3 - - + -
613B LEU* 4.0 33.0 - - + +
616B GLU* 6.3 0.7 - - + -
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Residues in contact with GLN 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 ILE* 3.1 37.9 + - + +
594B LYS* 4.0 6.7 - - - +
596B PHE* 1.3 73.7 - - + +
598B ARG* 1.3 54.9 + - - +
600B ILE* 3.2 9.9 + - + +
601B GLN* 2.5 36.1 + - - +
613B LEU* 6.0 4.3 - - + -
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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
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576B TRP* 4.2 25.0 - - + -
594B LYS 3.4 11.1 + - - +
595B PHE* 3.0 12.4 + - - +
597B GLN* 1.3 75.1 - - - +
599B ALA* 1.3 58.0 + - - +
601B GLN* 3.3 10.9 - - + +
602B VAL* 2.7 35.2 + - - +
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Residues in contact with ALA 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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573B PRO* 3.5 31.3 - - + +
576B TRP* 3.6 24.8 - - + +
577B CYS* 4.0 6.1 - - - +
595B PHE 2.9 9.0 + - - +
596B PHE* 3.4 11.9 - - - +
598B ARG* 1.3 75.0 - - - +
600B ILE* 1.3 58.3 + - - +
602B VAL* 3.2 1.4 + - - +
603B ASP 2.9 25.5 + - - +
609B ALA* 3.7 17.3 - - + -
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Residues in contact with ILE 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 PHE 3.1 9.8 + - - +
597B GLN* 3.3 12.6 - - + +
599B ALA* 1.3 77.2 - - - +
601B GLN* 1.3 60.8 + - - +
603B ASP 3.8 7.6 - - - -
604B PRO* 2.9 33.3 - - - +
609B ALA* 4.1 7.3 - - + +
610B TYR* 3.7 33.2 - - + +
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Residues in contact with GLN 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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597B GLN 2.5 19.8 + - - +
598B ARG* 3.1 14.1 + - + +
600B ILE* 1.3 74.0 - - - +
602B VAL* 1.3 62.0 + - - +
603B ASP* 4.6 0.2 - - - -
604B PRO* 4.7 1.9 - - - +
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Residues in contact with VAL 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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570B LYS 4.7 0.9 - - - +
571B ASN* 3.8 35.8 - - - +
573B PRO 4.6 4.3 - - - -
576B TRP* 4.5 11.4 - - + +
598B ARG 2.7 18.1 + - - +
599B ALA 3.7 4.5 - - - +
601B GLN* 1.3 74.6 - - - +
603B ASP* 1.3 61.3 + - - +
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Residues in contact with ASP 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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571B ASN 5.8 0.9 - - - +
573B PRO* 4.2 9.4 - - + -
599B ALA 2.9 11.6 + - - +
600B ILE* 3.1 8.5 - - - +
602B VAL* 1.3 80.4 - - + +
604B PRO* 1.3 61.2 - - - +
605B ASN* 3.0 7.4 - - + +
606B TYR* 3.0 34.4 + - + +
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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