Contacts of the strand formed by residues 1006 - 1012 (chain A) in PDB entry 1HXK
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 VAL1006 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1000A CYS* 3.5 22.7 - - + +
1001A HIS* 3.4 36.6 - - + +
1003A LEU 4.5 2.2 - - - +
1004A PRO* 3.4 2.0 - - + -
1005A ASN* 1.3 74.9 - - - +
1007A ALA* 1.3 60.9 + - - +
1008A ARG 3.5 25.8 - - - +
1026A MET* 3.1 30.7 - - + +
1041A SER* 4.4 2.5 - - - -
1042A SER 3.4 7.6 - - - +
1043A HIS* 3.5 10.5 - - + -
1044A SER* 5.6 0.2 - - - -
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Residues in contact with ALA1007 (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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972A THR* 5.7 1.3 - - + -
1005A ASN 3.4 1.0 + - - -
1006A VAL* 1.3 73.5 - - - +
1008A ARG* 1.3 82.1 + - - +
1022A HIS* 5.6 0.7 - - - -
1026A MET* 3.7 12.3 - - - +
1042A SER* 2.7 18.5 + - - +
1043A HIS 4.8 0.2 - - - -
1044A SER* 4.4 22.9 - - - +
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Residues in contact with ARG1008 (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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972A THR* 4.4 11.1 + - - +
1006A VAL* 3.5 8.5 - - - +
1007A ALA* 1.3 97.1 + - - +
1009A CYS* 1.3 60.5 + - - +
1010A GLU* 3.8 24.9 - - - +
1022A HIS* 4.3 21.8 - - + +
1026A MET* 4.1 9.2 - - - -
1040A VAL 4.6 0.2 - - - -
1041A SER* 3.4 3.5 - - - -
1042A SER* 2.9 57.9 + - - +
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Residues in contact with CYS1009 (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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1000A CYS* 2.0 48.5 - - + -
1008A ARG* 1.3 75.0 - - - +
1010A GLU* 1.3 66.2 + - - +
1022A HIS* 3.9 3.0 + - - -
1023A LEU* 2.9 52.2 + - + +
1026A MET* 3.5 27.6 - - - +
1027A VAL 4.1 0.4 - - - +
1028A ALA* 3.6 12.6 - - - -
1039A TYR* 4.7 1.3 - - - -
1040A VAL 3.6 1.3 - - - -
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Residues in contact with GLU1010 (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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974A ARG* 5.1 4.2 + - - -
1008A ARG* 3.8 25.7 - - - +
1009A CYS* 1.3 81.6 - - - +
1011A ARG* 1.3 63.5 + - - +
1012A THR* 3.8 2.8 + - + +
1019A ASN* 3.6 41.9 + - + +
1021A GLU 3.1 12.6 - - - +
1022A HIS* 4.5 14.5 + - - +
1023A LEU* 4.2 4.9 - - - -
1039A TYR* 3.2 4.7 - - - +
1040A VAL* 2.9 43.8 + - + +
1042A SER* 4.3 6.8 + - - -
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Residues in contact with ARG1011 (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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1010A GLU* 1.3 74.3 - - - +
1012A THR* 1.3 60.2 + - - +
1019A ASN* 3.7 1.4 - - - -
1020A LEU* 2.7 44.3 + - + -
1021A GLU* 2.7 57.8 + - + +
1023A LEU* 4.1 8.7 - - + +
1029A PRO* 4.1 18.6 - - - +
1031A VAL* 5.3 1.0 - - - +
1035A GLU* 5.9 1.8 + - - -
1037A ALA* 4.1 13.4 - - + +
1038A ALA 3.4 12.3 - - - +
1039A TYR* 2.9 38.4 + - + -
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Residues in contact with THR1012 (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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1010A GLU 3.9 7.4 - - - +
1011A ARG* 1.3 81.5 - - - +
1013A THR* 1.3 75.2 + - - +
1014A LEU* 3.8 0.9 + - - +
1016A PHE* 3.5 20.9 - - - +
1018A GLN 3.1 12.6 - - - +
1019A ASN* 3.5 24.2 - - - +
1020A LEU* 3.7 12.4 - - - +
1038A ALA* 2.9 33.0 + - - +
1040A VAL* 3.7 24.2 - - + +
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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