Contacts of the helix formed by residues 596 - 608 (chain A) in PDB entry 1HS6
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 HIS 596 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113A SER 4.1 5.9 + - - -
114A ALA 5.1 1.6 - - - -
115A LEU 4.8 4.5 - - - -
116A GLN* 3.3 30.7 + - + +
132A PHE* 3.7 21.4 - + - -
134A GLN* 4.5 12.9 - - + +
264A SER* 3.8 14.4 - - - +
266A PRO* 3.6 26.8 - - + +
595A MET* 1.3 77.1 - - - +
597A PRO* 1.3 76.6 - - + +
598A VAL* 3.0 43.9 + - + +
599A THR* 3.7 20.0 - - - +
600A ALA* 2.8 26.9 + - - +
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Residues in contact with PRO 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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111A LYS 5.1 5.2 - - - +
112A SER 3.8 9.6 - - - +
113A SER* 3.9 23.8 - - - +
115A LEU 3.1 28.3 - - - +
116A GLN* 4.2 5.2 - - + -
595A MET 3.4 4.5 - - - +
596A HIS* 1.3 93.0 - - + +
598A VAL* 1.3 63.8 + - - +
600A ALA* 3.7 6.0 - - + +
601A MET* 3.0 22.3 + - - +
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Residues in contact with VAL 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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113A SER* 3.7 25.1 - - - +
134A GLN* 6.6 0.2 - - + -
139A HIS* 3.8 26.2 - - + +
266A PRO* 5.8 0.7 - - + -
267A TYR* 5.1 1.6 - - + +
375A ASP* 3.6 27.6 - - + +
564A MET* 4.3 12.6 - - + -
596A HIS* 3.0 14.6 - - + +
597A PRO* 1.3 75.9 - - - +
599A THR* 1.3 70.1 + - - +
601A MET* 3.0 9.3 + - + +
602A LEU* 2.8 39.1 + - + +
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Residues in contact with THR 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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266A PRO* 3.7 9.4 - - - +
562A GLY* 4.0 14.8 + - - +
564A MET* 3.5 34.2 - - + +
567A THR* 4.4 12.6 - - + -
568A ARG* 5.3 0.7 - - + -
595A MET* 5.1 9.2 - - + -
596A HIS* 3.5 25.8 + - - +
597A PRO 3.4 0.2 - - - -
598A VAL* 1.3 79.5 - - - +
600A ALA* 1.3 63.0 + - - +
602A LEU* 3.2 1.6 + - - +
603A VAL* 2.9 40.2 + - + +
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Residues in contact with ALA 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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588A TYR* 2.8 28.0 + - - +
592A LYS* 4.2 12.6 - - + +
595A MET* 4.1 24.0 - - + +
596A HIS 2.8 19.7 + - - +
597A PRO* 3.7 9.0 - - + +
599A THR* 1.3 78.5 - - - +
601A MET* 1.3 63.8 + - - +
604A GLY 3.2 7.8 + - - -
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Residues in contact with MET 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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373A ASP* 3.8 22.0 - - - +
375A ASP* 4.4 9.6 - - + +
376A VAL* 4.4 5.4 - - + -
588A TYR* 5.0 0.2 - - - -
597A PRO 3.0 13.6 + - - +
598A VAL* 3.0 10.1 + - + +
600A ALA* 1.3 81.3 - - - +
602A LEU* 1.3 92.3 + - + +
604A GLY* 4.0 1.1 - - - -
605A LYS* 3.2 34.5 + - + +
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Residues in contact with LEU 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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375A ASP* 3.8 23.6 - - + +
376A VAL* 4.1 14.4 - - + -
564A MET* 3.6 30.5 - - + -
568A ARG* 3.7 38.1 + - - +
598A VAL* 2.8 29.1 + - + +
599A THR* 3.9 3.1 - - - +
601A MET* 1.3 98.0 - - + +
603A VAL* 1.3 52.3 + - - +
605A LYS* 3.2 7.6 + - + +
606A ASP* 2.7 40.5 + - - -
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Residues in contact with VAL 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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567A THR* 4.1 13.7 - - + -
568A ARG* 4.0 24.9 - - + -
571A PHE* 3.9 21.1 - - + -
588A TYR* 3.4 29.4 - - + -
595A MET* 5.3 2.2 - - - -
599A THR* 2.9 35.4 + - + +
600A ALA* 4.9 0.2 - - - -
602A LEU* 1.3 71.2 - - - +
604A GLY* 1.3 52.2 + - - +
606A ASP* 3.1 7.3 + - + +
607A LEU* 2.6 52.6 + - + +
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Residues in contact with GLY 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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588A TYR* 3.3 29.0 + - - -
600A ALA 3.2 10.1 + - - -
601A MET 4.0 2.5 - - - -
603A VAL* 1.3 75.3 - - - +
605A LYS* 1.3 57.9 + - - +
607A LEU 3.2 0.3 + - - -
608A LYS* 2.8 23.6 + - - -
609A VAL* 2.8 25.8 + - - +
610A ASP* 5.0 2.0 - - - -
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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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376A VAL* 4.5 29.0 - - + +
601A MET* 3.2 30.9 + - - +
602A LEU* 3.3 12.3 - - + +
604A GLY* 1.3 74.7 - - - +
606A ASP* 1.3 69.4 + - - +
608A LYS* 2.8 20.4 + - - +
609A VAL 5.2 0.7 - - - -
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Residues in contact with ASP 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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568A ARG* 2.8 51.3 + - - +
571A PHE* 6.0 0.7 - - + -
572A LYS* 2.9 44.2 + - + +
602A LEU 2.7 19.4 + - - +
603A VAL* 3.3 9.9 - - + +
605A LYS* 1.3 75.9 - - - +
607A LEU* 1.3 67.7 + - + +
608A LYS* 3.4 8.1 + - - +
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Residues in contact with LEU 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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571A PHE* 3.8 30.3 - - + +
572A LYS* 4.5 2.9 - - + -
575A ALA* 3.8 26.0 - - + -
581A HIS* 6.0 0.3 + - - -
584A ALA* 4.3 6.3 - - + +
585A VAL* 4.4 19.7 - - + +
588A TYR* 3.8 23.3 - - + -
603A VAL* 2.6 37.0 + - + +
606A ASP* 1.3 80.1 - - + +
608A LYS* 1.3 73.9 + - - +
609A VAL* 3.2 21.4 + - + +
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Residues in contact with LYS 608 (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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604A GLY 2.8 6.1 + - - -
605A LYS* 2.8 15.4 + - - +
606A ASP 4.3 6.3 - - - +
607A LEU* 1.3 83.3 - - - +
609A VAL* 1.3 62.6 + - - +
610A ASP 4.0 1.7 + - - +
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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