Contacts of the strand formed by residues 1002 - 1010 (chain A) in PDB entry 4Z96
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 THR1002 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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946A SER* 2.7 32.7 + - - -
947A TYR* 3.5 16.4 - - - -
948A LYS* 3.9 16.9 - - + +
993A ALA* 4.7 0.9 - - + -
994A HIS 3.6 16.4 - - - +
995A PHE* 4.1 2.9 - - + -
999A VAL 4.1 9.0 - - - +
1000A PHE* 3.1 9.4 + - - -
1001A GLY* 1.3 78.9 - - - +
1003A PHE* 1.3 65.8 + - - +
1076A TRP* 3.8 28.7 - - + -
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Residues in contact with PHE1003 (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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947A TYR* 3.5 20.8 - - + +
994A HIS* 3.2 32.7 + + + +
995A PHE* 3.4 39.7 - - - -
996A HIS* 4.1 5.2 - - + -
1001A GLY 4.2 3.4 - - - -
1002A THR* 1.3 79.7 - - - +
1004A GLY* 1.3 84.6 + - - +
1005A ILE 5.0 0.2 - - - -
1081A HIS* 3.7 25.1 - + - -
1082A PHE 3.2 21.8 - - - -
1083A ASN* 3.3 30.3 - - - +
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Residues in contact with GLY1004 (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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947A TYR* 3.2 24.6 - - - +
994A HIS* 4.7 4.7 - - - -
1003A PHE* 1.3 92.8 - - - +
1005A ILE* 1.3 64.1 + - - -
1006A PRO* 3.3 10.4 - - - +
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Residues in contact with ILE1005 (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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899A LEU* 4.5 5.8 - - + -
903A PHE* 3.7 46.3 - - + +
904A ARG* 5.0 0.7 - - - -
905A GLU* 3.8 37.0 - - + +
971A ARG* 3.3 25.4 - - - +
994A HIS* 3.6 20.2 + - - +
1003A PHE 3.9 0.4 + - - -
1004A GLY* 1.3 74.5 - - - -
1006A PRO* 1.3 68.9 - - - +
1007A PHE* 3.5 13.0 - - - -
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Residues in contact with PRO1006 (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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903A PHE* 4.6 0.2 - - - -
905A GLU* 5.4 1.1 - - - +
944A ILE* 3.9 25.1 - - + -
947A TYR* 3.2 31.6 - - - +
948A LYS* 4.2 0.4 - - - -
949A ILE* 3.8 20.2 - - + +
971A ARG* 3.0 25.7 + - - +
992A VAL 3.2 19.3 - - - +
993A ALA* 4.5 3.1 - - - -
1004A GLY 3.3 10.1 - - - +
1005A ILE* 1.3 92.0 - - - +
1007A PHE* 1.3 66.1 + - + +
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Residues in contact with PHE1007 (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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903A PHE* 3.8 25.6 - + + -
949A ILE* 3.5 13.5 - - - +
971A ARG* 4.0 5.6 - - - +
973A GLU* 5.7 0.7 - - - +
991A THR* 3.5 1.7 - - - -
992A VAL* 2.7 72.5 + - + -
994A HIS* 4.5 14.6 - + - -
1005A ILE 3.5 17.9 - - - -
1006A PRO* 1.3 77.6 - - + +
1008A LEU* 1.3 70.5 + - - +
1009A LEU* 4.3 16.4 - - + -
1024A ILE* 4.3 22.4 - - + -
1027A LEU* 4.4 22.7 - - + -
1028A LEU* 6.2 1.6 - - + -
1079A LEU* 4.5 2.9 - - + -
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Residues in contact with LEU1008 (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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940A ARG* 3.5 45.0 + - - +
942A LEU* 4.4 4.0 - - + -
949A ILE* 3.8 17.7 - - + +
952A VAL* 4.0 24.5 - - + -
973A GLU* 5.2 0.8 + - - -
979A GLN* 3.1 23.2 + - - +
989A LEU* 4.6 16.8 - - + +
990A VAL* 3.2 6.3 - - - +
991A THR* 3.6 33.4 - - + +
1007A PHE* 1.3 83.6 - - - +
1009A LEU* 1.3 62.3 + - - +
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Residues in contact with LEU1009 (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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979A GLN* 4.3 6.1 + - - +
988A MET 3.3 0.5 - - - +
989A LEU* 3.3 32.4 - - - +
990A VAL* 2.5 32.0 + - + +
992A VAL* 3.7 19.5 - - + -
1007A PHE* 4.3 9.0 - - + -
1008A LEU* 1.3 80.2 - - - +
1010A ARG* 1.3 80.0 + - + +
1020A VAL* 4.5 10.1 - - + -
1023A ARG* 4.6 21.1 - - + +
1024A ILE* 3.5 33.0 - - + -
1027A LEU* 5.7 6.5 - - + -
1077A LEU* 4.4 9.4 - - + -
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Residues in contact with ARG1010 (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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978A ASP* 2.5 57.7 + - - +
979A GLN* 5.7 4.9 - - + +
987A GLU* 4.6 19.6 + - + +
988A MET 3.6 3.4 - - - -
1009A LEU* 1.3 91.6 - - + +
1011A ILE* 1.3 62.6 + - - +
1013A GLN 5.6 0.3 - - - +
1020A VAL* 5.2 6.8 - - - +
1023A ARG* 3.1 44.5 + - - +
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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