Contacts of the helix formed by residues 591 - 605 (chain A) in PDB entry 4G2W
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 LYS 591 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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589A GLN 3.5 7.8 + - - +
590A MET* 1.3 74.5 - - - +
592A HIS* 1.3 67.4 + - - +
593A GLU* 3.3 19.5 - - - +
594A VAL* 3.0 37.2 + - + +
595A LEU* 3.0 13.1 + - - +
702A SER* 4.5 14.1 + - - -
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Residues in contact with HIS 592 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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543A LEU 4.5 2.6 + - - -
544A ALA* 3.5 29.6 + - + -
546A ALA 4.8 5.5 + - - -
548A VAL* 4.9 8.1 - - + -
576A ILE* 4.4 23.8 - - + +
585A VAL* 6.3 2.2 - - - +
590A MET 3.8 3.0 + - - -
591A LYS* 1.3 73.8 - - - +
593A GLU* 1.3 65.7 + - + +
595A LEU* 3.2 10.0 + - + +
596A CYS* 2.9 50.4 + - - -
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Residues in contact with GLU 593 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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540A LEU* 4.7 7.8 - - + +
544A ALA* 5.0 11.2 - - + -
591A LYS* 4.0 23.9 - - - +
592A HIS* 1.3 86.0 + - + +
594A VAL* 1.3 66.8 + - + +
596A CYS* 3.8 9.6 - - - +
597A ARG* 3.0 44.1 + - - +
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Residues in contact with VAL 594 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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591A LYS* 3.0 35.1 + - + +
593A GLU* 1.3 84.5 - - + +
595A LEU* 1.3 59.9 + - - +
597A ARG* 3.2 3.3 + - - +
598A TRP* 2.8 28.8 + - - +
697A GLY* 3.2 28.6 - - - +
698A ASN 3.7 0.9 - - - -
699A GLN* 3.5 37.0 - - + +
700A ILE* 3.8 6.3 - - + +
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Residues in contact with LEU 595 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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576A ILE* 4.4 23.1 - - + -
579A PHE* 4.0 36.8 - - + -
585A VAL* 3.8 28.7 - - + -
590A MET* 4.4 9.0 - - + -
591A LYS 3.0 11.2 + - - +
592A HIS* 3.5 14.1 - - - +
594A VAL* 1.3 76.6 - - - +
596A CYS* 1.3 63.0 + - - +
598A TRP* 3.0 5.9 + - + +
599A ILE* 2.9 45.4 + - + +
700A ILE* 3.7 22.3 - - + +
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Residues in contact with CYS 596 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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540A LEU* 4.8 5.6 - - + -
543A LEU* 3.7 19.0 - - + +
544A ALA* 3.9 22.0 - - + +
576A ILE* 3.8 19.7 - - - -
592A HIS* 2.9 46.4 + - - +
593A GLU* 3.8 7.6 - - - +
595A LEU* 1.3 75.8 - - - +
597A ARG* 1.3 63.1 - - - +
599A ILE* 3.3 6.7 + - - +
600A LEU* 3.0 28.1 + - - +
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Residues in contact with ARG 597 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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540A LEU* 3.5 37.6 - - + +
593A GLU* 3.0 41.9 + - - +
594A VAL* 3.2 4.9 + - - +
596A CYS* 1.3 76.1 - - - +
598A TRP* 1.3 58.6 + - - +
600A LEU* 3.2 5.5 + - + +
601A SER* 2.8 29.8 + - - +
696A PRO 4.3 2.0 - - - -
697A GLY* 3.3 32.0 + - - +
698A ASN* 2.9 32.1 - - - +
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Residues in contact with TRP 598 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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579A PHE* 3.7 25.4 - + - -
594A VAL 2.8 18.3 + - - +
595A LEU* 3.0 8.3 + - + +
597A ARG* 1.3 77.2 - - - +
599A ILE* 1.3 81.2 + - + +
601A SER* 3.2 2.4 + - - -
602A VAL* 2.8 49.7 + - + +
648A ILE* 4.0 19.3 - - + -
651A LEU* 3.7 29.6 - - + -
652A SER* 3.9 12.1 - - - -
689A CYS* 5.2 1.1 + - - -
692A ILE* 3.3 28.5 - - + +
693A LEU* 3.7 19.6 - - + +
698A ASN* 3.2 30.4 + - + +
700A ILE* 3.6 26.9 - - + -
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Residues in contact with ILE 599 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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543A LEU* 5.0 2.0 - - + -
572A ALA* 4.0 28.7 - - + +
575A THR* 3.9 29.4 - - + -
576A ILE* 3.5 36.6 - - + +
579A PHE* 5.0 0.2 - - + -
595A LEU* 2.9 28.7 + - + +
596A CYS* 3.7 6.7 - - - +
598A TRP* 1.3 91.8 - - + +
600A LEU* 1.3 59.6 + - + +
602A VAL* 3.2 4.8 + - - +
603A LYS* 2.8 29.9 + - + +
615A TRP* 4.4 13.6 - - + -
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Residues in contact with LEU 600 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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539A GLU* 3.9 34.3 - - + +
540A LEU* 3.6 44.9 - - + +
543A LEU* 3.8 21.3 - - + -
572A ALA* 4.8 7.4 - - + -
596A CYS 3.0 19.1 + - - +
597A ARG* 3.6 6.1 - - + +
599A ILE* 1.3 76.6 - - - +
601A SER* 1.3 58.0 + - - +
603A LYS* 3.7 17.0 - - + +
604A LYS* 2.8 33.1 + - - +
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Residues in contact with SER 601 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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597A ARG* 2.8 14.3 + - - +
598A TRP 3.4 4.5 - - - -
600A LEU* 1.3 74.4 - - - +
602A VAL* 1.3 66.0 + - - +
604A LYS* 3.2 9.2 + - - +
605A ASN* 3.1 29.9 + - - +
692A ILE* 3.7 19.3 - - - -
698A ASN* 2.6 34.3 + - - -
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Residues in contact with VAL 602 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598A TRP* 2.8 61.7 + - + +
599A ILE* 3.2 5.8 + - - +
601A SER* 1.3 70.6 - - - +
603A LYS* 1.3 66.3 + - - +
605A ASN* 2.9 13.5 + - - -
606A TYR* 3.5 21.5 + - + -
615A TRP* 3.9 11.4 - - + -
651A LEU* 3.5 30.3 - - + +
652A SER* 4.5 4.0 - - - +
655A LEU* 3.6 7.8 - - + +
692A ILE* 4.1 16.8 - - + -
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Residues in contact with LYS 603 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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539A GLU* 3.4 33.0 + - - -
568A ASP* 3.0 39.9 + - + +
572A ALA* 5.5 3.1 - - + -
599A ILE* 2.8 21.5 + - + +
600A LEU* 3.7 19.7 - - + +
602A VAL* 1.3 73.0 - - - +
604A LYS* 1.3 62.3 - - - +
606A TYR* 3.3 19.6 + - - +
615A TRP* 3.6 57.1 - - + +
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Residues in contact with LYS 604 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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600A LEU 2.8 19.8 + - - +
601A SER* 3.5 8.7 - - - +
602A VAL 3.1 0.2 - - - -
603A LYS* 1.3 78.6 - - - +
605A ASN* 1.3 70.0 + - - +
606A TYR 3.2 12.8 - - - +
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Residues in contact with ASN 605 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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601A SER* 3.1 26.1 + - - +
602A VAL 2.9 6.2 + - - -
604A LYS* 1.3 89.6 - - - +
606A TYR* 1.3 59.1 + - - +
607A ARG* 5.2 0.8 - - - +
655A LEU* 3.8 19.5 - - + -
656A ASP* 2.9 32.0 + - + +
688A GLN* 4.0 17.5 - - - +
692A ILE* 4.0 17.4 - - + +
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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