Contacts of the helix formed by residues 665 - 672 (chain A) in PDB entry 1H5P
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 THR 665 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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656A LYS 2.7 22.1 + - - -
657A LEU* 3.9 22.8 - - + +
659A ILE 3.1 17.5 - - - +
660A ARG* 3.7 16.4 - - + +
663A GLY 5.4 1.1 - - - +
664A TYR* 1.3 78.1 - - - +
666A LEU* 1.3 60.1 + - - +
667A LYS* 3.2 14.0 + - - +
668A VAL* 3.1 13.8 + - + +
669A LEU* 2.8 24.8 + - - +
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Residues in contact with LEU 666 (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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607A VAL* 5.1 2.5 - - + -
616A LEU* 5.3 5.6 - - + -
621A PHE* 4.6 16.6 - - + -
630A ILE* 6.4 1.1 - - + -
640A PRO* 5.6 4.9 - - + -
655A TRP* 3.8 33.2 - - + +
656A LYS* 3.2 5.3 + - - +
659A ILE* 3.5 43.3 - - + +
660A ARG 4.4 4.3 - - - +
661A CYS* 4.5 7.4 - - + -
665A THR* 1.3 72.7 - - - +
667A LYS* 1.3 57.6 + - - +
669A LEU* 3.6 25.5 - - + -
670A MET* 2.7 38.4 + - + +
675A LEU* 5.6 5.3 - - + +
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Residues in contact with LYS 667 (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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654A ASN* 6.1 1.6 - - - +
656A LYS* 2.8 64.0 + - + +
657A LEU* 3.5 26.7 - - + -
665A THR* 3.4 6.1 - - - +
666A LEU* 1.3 79.0 - - - +
668A VAL* 1.3 61.6 + - + +
670A MET* 3.0 35.5 - - - +
671A GLU* 3.3 26.1 + - - +
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Residues in contact with VAL 668 (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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657A LEU* 6.0 1.3 - - + -
664A TYR* 3.9 22.7 - - + -
665A THR* 3.1 21.9 + - + +
667A LYS* 1.3 79.0 - - + +
669A LEU* 1.3 52.8 + - - +
670A MET 3.0 1.8 - - - -
671A GLU* 2.8 19.6 + - + +
672A ASN* 2.7 34.3 + - - +
687A ILE* 4.0 18.2 - - + -
688A LYS 3.2 24.9 - - - +
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Residues in contact with LEU 669 (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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598A ILE* 6.0 2.5 - - + -
605A LEU* 4.2 9.4 - - + -
621A PHE* 4.8 6.1 - - + -
661A CYS* 3.4 39.7 - - + +
664A TYR* 3.1 38.6 - - + +
665A THR 2.8 12.4 + - - +
666A LEU* 3.2 20.4 + - + +
668A VAL* 1.3 71.7 - - - +
670A MET* 1.3 58.7 + - - +
672A ASN* 2.6 22.1 - - - +
673A LYS 3.8 0.7 + - - -
674A PHE* 3.4 37.3 + - + -
675A LEU* 3.0 25.8 + - + -
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Residues in contact with MET 670 (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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655A TRP* 4.5 13.5 - - + -
656A LYS* 4.3 26.9 - - + -
666A LEU* 2.7 14.3 + - + +
667A LYS* 3.0 37.9 - - - +
669A LEU* 1.3 77.1 - - - +
671A GLU* 1.3 62.3 + - + +
672A ASN 5.2 0.2 - - - -
673A LYS* 5.1 0.8 - - - -
675A LEU* 3.3 34.1 - - + +
676A PRO 5.0 2.1 - - - +
677A GLU* 3.4 31.0 - - + +
680A SER* 3.7 18.2 - - - -
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Residues in contact with GLU 671 (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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667A LYS* 3.3 31.6 + - - +
668A VAL* 2.8 13.4 + - + +
670A MET* 1.3 82.5 - - - +
672A ASN* 1.3 62.9 + - - +
680A SER* 4.7 14.6 + - - +
681A THR* 4.7 22.5 + - - +
685A VAL* 5.5 9.8 - - + +
686A THR 5.4 8.1 - - - +
687A ILE* 5.2 11.9 - - + +
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Residues in contact with ASN 672 (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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664A TYR* 4.9 2.0 - - - +
668A VAL* 2.7 27.9 + - - +
669A LEU* 2.6 33.9 - - - +
670A MET 5.1 0.7 - - - -
671A GLU* 1.3 81.2 - - - +
673A LYS* 1.3 86.2 + - - +
674A PHE* 3.1 22.8 - - - -
680A SER* 5.3 3.3 + - - -
687A ILE 5.1 4.0 - - - -
688A LYS* 3.1 42.6 + - - +
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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