Contacts of the helix formed by residues 596 - 607 (chain A) in PDB entry 2H5G
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 596 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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593A SER* 3.0 18.3 + - - +
595A ASP* 1.3 83.8 - - + +
597A VAL* 1.3 67.4 + - - +
598A THR 3.4 2.6 + - - -
599A ARG* 3.5 12.4 - - - +
600A LEU* 3.3 35.8 + - + +
700A VAL* 4.8 4.5 - - + -
702A GLU* 2.7 38.9 + - - +
722A ASN* 3.4 26.0 - - + +
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Residues in contact with VAL 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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588A VAL* 4.1 13.7 - - + -
592A ALA* 3.8 24.9 - - + -
593A SER 3.2 16.8 + - - +
594A VAL* 4.2 3.4 + - - +
595A ASP 3.9 0.4 - - - -
596A LYS* 1.3 76.4 - - - +
598A THR* 1.3 65.8 + - - +
600A LEU* 3.1 4.5 + - - +
601A VAL* 2.9 30.9 + - + +
629A LEU* 3.8 19.7 - - + -
633A ILE* 3.5 33.4 - - + -
700A VAL* 4.1 13.5 - - + -
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Residues in contact with THR 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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594A VAL 5.0 6.4 + - - -
595A ASP 5.5 0.6 - - - -
596A LYS 3.4 0.4 - - - -
597A VAL* 1.3 80.2 - - - +
599A ARG* 1.3 58.0 + - - +
601A VAL* 4.8 0.7 - - - -
602A ARG* 2.8 44.0 + - - +
629A LEU 5.0 0.7 + - - -
632A GLN* 3.8 31.6 + - + +
633A ILE* 4.2 6.4 + - - +
636A MSE 3.4 40.8 - - + +
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Residues in contact with ARG 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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305A SO4 3.2 51.4 + - - +
595A ASP 4.3 15.7 - - - -
596A LYS* 3.5 13.2 - - - +
598A THR* 1.3 78.7 - - - +
600A LEU* 1.3 66.7 + - + +
602A ARG* 3.4 14.8 + - - +
603A ASP* 2.9 30.5 + - - +
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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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586A MSE 4.0 14.6 - - + -
596A LYS* 3.4 23.8 - - + +
597A VAL 3.1 8.1 + - - +
599A ARG* 1.3 83.7 - - + +
601A VAL* 1.3 63.9 + - - +
603A ASP* 4.0 2.7 - - + +
604A SER* 2.8 31.5 + - - -
700A VAL* 3.8 31.4 - - + -
722A ASN* 4.2 18.4 - - + +
723A ALA* 3.7 11.7 - - - -
724A SER* 3.5 31.8 + - - +
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Residues in contact with VAL 601 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586A MSE 3.8 20.6 - - - -
588A VAL* 4.8 0.2 - - + -
597A VAL* 2.9 32.1 + - + +
598A THR* 4.6 0.4 - - - -
600A LEU* 1.3 73.4 - - - +
602A ARG* 1.3 66.6 + - - +
604A SER* 3.9 2.4 - - - -
605A LYS* 3.1 23.8 + - + +
615A LEU* 4.0 15.9 - - + +
618A LEU* 4.0 29.2 - - + -
633A ILE* 4.7 4.9 - - + -
636A MSE 3.6 21.8 - - + -
637A LEU* 4.4 9.9 - - + -
673A LEU* 4.7 1.3 - - + -
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Residues in contact with ARG 602 (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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305A SO4 3.9 11.1 + - - -
598A THR* 2.8 31.3 + - - +
599A ARG* 3.4 35.9 - - - +
601A VAL* 1.3 72.9 - - - +
603A ASP* 1.3 53.5 + - - +
606A CYS* 2.7 46.3 + - + +
607A GLU 3.7 0.3 + - - -
636A MSE 3.3 43.9 - - + +
639A VAL* 6.2 1.0 - - - +
640A GLU* 4.0 20.9 + - - +
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Residues in contact with ASP 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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599A ARG 2.9 19.1 + - - +
600A LEU* 4.0 2.2 - - + +
602A ARG* 1.3 76.5 - - - +
604A SER* 1.3 63.8 + - - +
607A GLU* 3.1 52.3 + - - +
724A SER* 2.7 32.1 + - - +
726A ARG* 3.7 12.5 - - - +
727A PHE* 5.2 2.9 - - - -
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Residues in contact with SER 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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586A MSE 3.3 14.1 - - - +
600A LEU 2.8 22.5 + - - -
601A VAL 3.9 2.7 - - - -
603A ASP* 1.3 76.8 - - - +
605A LYS* 1.3 58.0 + - - +
608A TYR 5.4 0.2 - - - +
614A ALA* 3.4 11.3 - - - +
615A LEU* 2.9 36.4 + - - -
724A SER* 3.2 7.1 + - - -
725A THR* 3.1 38.8 + - - -
726A ARG* 4.2 4.8 - - - +
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Residues in contact with LYS 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 VAL* 3.1 18.8 + - + +
602A ARG* 5.1 0.2 - - - -
604A SER* 1.3 79.9 - - - +
606A CYS* 1.3 75.9 + - - +
607A GLU 3.7 0.4 - - - -
608A TYR 4.3 0.8 - - - -
609A PRO* 3.5 22.1 + - - +
614A ALA* 4.7 3.8 - - - +
615A LEU* 2.6 38.3 + - + +
616A GLU* 3.7 13.5 + - - -
637A LEU* 5.2 2.9 - - + -
642A VAL* 4.4 13.9 - - + -
668A TYR* 4.7 0.2 - - - +
670A ASP 3.2 26.5 + - - +
671A LEU* 4.6 1.6 - - + +
672A GLU 3.0 26.2 + - - +
673A LEU* 4.0 17.9 - - + -
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Residues in contact with CYS 606 (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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602A ARG* 2.7 30.3 + - + +
605A LYS* 1.3 81.6 - - - +
607A GLU* 1.3 65.3 + - - +
608A TYR 3.1 3.0 + - - -
609A PRO* 3.6 14.2 - - - +
636A MSE 4.7 2.9 - - - -
637A LEU* 5.7 0.4 - - - -
640A GLU* 3.0 45.3 - - + +
642A VAL* 3.9 17.9 - - - -
671A LEU* 4.4 6.3 - - + +
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Residues in contact with GLU 607 (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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602A ARG 3.7 2.2 + - - -
603A ASP* 3.1 42.7 + - - +
606A CYS* 1.3 78.8 - - - +
608A TYR* 1.3 61.1 + - - +
609A PRO* 4.4 0.7 - - - +
726A ARG* 2.8 44.3 + - - +
732A ARG* 5.8 1.5 + - - -
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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