Contacts of the strand formed by residues 1002 - 1011 (chain C) in PDB entry 4YOC
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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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946C SER* 2.7 33.3 + - - +
947C TYR* 3.3 19.8 - - - -
948C LYS* 4.2 18.7 - - + +
994C HIS 3.3 18.8 - - - +
995C PHE* 3.8 4.9 - - + +
996C HIS* 4.0 4.7 - - - -
999C VAL 3.5 23.1 - - - +
1000C PHE 3.2 7.6 + - - +
1001C GLY* 1.3 73.3 - - - +
1003C PHE* 1.3 67.6 + - - +
1076C TRP* 4.4 5.2 - - + -
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Residues in contact with PHE1003 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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947C TYR* 3.6 21.6 - - + +
994C HIS* 3.2 30.2 + + + +
995C PHE* 3.4 29.2 - - - -
996C HIS* 3.5 26.7 - + + +
1002C THR* 1.3 82.0 - - - +
1004C GLY* 1.3 83.4 + - - +
1006C PRO* 5.2 0.3 - - - +
1081C HIS* 3.4 28.0 - + - -
1082C PHE* 3.1 34.1 - - - -
1083C ASN* 4.0 22.4 - - + +
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Residues in contact with GLY1004 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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905C GLU* 5.5 0.5 - - - +
947C TYR* 3.5 18.9 - - - +
994C HIS* 4.4 9.4 - - - -
1003C PHE* 1.3 95.5 - - - +
1005C ILE* 1.3 64.2 + - - +
1006C PRO* 3.3 10.6 - - - +
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Residues in contact with ILE1005 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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899C LEU* 4.6 7.2 - - + -
903C PHE* 3.8 50.0 - - + +
904C ARG* 4.9 0.7 - - + -
905C GLU* 3.7 42.0 - - + +
971C ARG* 3.4 24.5 - - - +
994C HIS* 4.2 14.0 + - - -
1003C PHE 5.2 0.2 - - - -
1004C GLY* 1.3 73.9 - - - +
1006C PRO* 1.3 66.4 - - + +
1007C PHE* 3.6 12.6 - - - -
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Residues in contact with PRO1006 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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905C GLU* 5.4 2.0 - - - +
944C ILE* 3.8 19.1 - - + -
947C TYR* 3.4 33.4 - - + +
948C LYS* 4.3 0.9 - - - -
949C ILE* 3.8 22.0 - - + +
971C ARG* 2.8 32.1 + - - +
992C VAL 3.2 15.9 - - - +
993C ALA* 4.3 6.1 - - + -
1003C PHE 5.2 0.4 - - - -
1004C GLY 3.3 11.2 - - - +
1005C ILE* 1.3 91.0 - - + +
1007C PHE* 1.3 61.2 + - + +
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Residues in contact with PHE1007 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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903C PHE* 4.2 17.7 - + + -
949C ILE* 3.9 11.7 - - - +
971C ARG* 4.0 6.1 - - - +
991C THR* 3.8 0.9 - - - -
992C VAL* 2.9 73.1 + - + +
994C HIS* 4.1 20.6 - + - -
1005C ILE 3.6 13.5 - - - -
1006C PRO* 1.3 75.6 - - + +
1008C LEU* 1.3 71.5 + - - +
1009C LEU* 4.1 13.5 - - + -
1024C ILE* 4.0 29.8 - - + -
1027C LEU* 3.5 31.0 - - + -
1028C LEU* 4.4 4.5 - - + -
1079C LEU* 4.6 0.7 - - + -
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Residues in contact with LEU1008 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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940C ARG* 3.4 43.5 + - - +
942C LEU* 3.7 20.2 - - + -
949C ILE* 4.1 15.7 - - + +
952C VAL* 3.9 15.5 - - + -
971C ARG* 5.0 1.2 - - - +
973C GLU* 5.0 1.2 + - - +
976C PRO* 5.4 0.2 - - - +
979C GLN* 2.9 21.7 + - - +
989C LEU* 5.1 12.8 - - + +
990C VAL 3.5 17.9 - - - +
991C THR* 3.7 20.2 - - - +
1007C PHE* 1.3 83.1 - - - +
1009C LEU* 1.3 60.2 + - - +
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Residues in contact with LEU1009 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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979C GLN* 3.9 2.5 - - - +
989C LEU* 3.5 3.2 - - - -
990C VAL* 2.9 39.9 + - + +
992C VAL* 3.7 15.9 - - + -
1007C PHE* 4.0 9.2 + - + -
1008C LEU* 1.3 75.2 - - - +
1010C ARG* 1.3 74.5 + - - +
1011C ILE* 4.9 1.6 - - + -
1020C VAL* 4.0 16.2 - - + -
1023C ARG* 3.7 33.4 - - + +
1024C ILE* 3.5 38.4 - - + +
1077C LEU* 4.4 13.7 - - + -
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Residues in contact with ARG1010 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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978C ASP* 3.2 57.9 + - - +
979C GLN* 3.8 7.3 - - + +
982C ILE* 4.4 2.2 - - + -
987C GLU* 3.5 39.4 + - + +
988C MET 4.8 0.2 - - - +
989C LEU* 3.8 18.6 - - + -
1009C LEU* 1.3 90.6 - - + +
1011C ILE* 1.3 70.5 + - - +
1012C HIS* 5.3 8.8 - - - +
1020C VAL* 4.0 0.2 - - - +
1023C ARG* 3.0 53.4 + - - +
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Residues in contact with ILE1011 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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986C ASN 3.9 0.5 - - - +
987C GLU* 3.1 11.2 - - - -
988C MET* 2.9 42.9 + - + +
990C VAL* 3.6 29.2 - - + -
1009C LEU* 4.9 2.0 - - + -
1010C ARG* 1.3 84.0 - - - +
1012C HIS* 1.3 74.2 + - - +
1015C GLU* 3.6 2.9 - - - +
1020C VAL* 4.4 14.8 - - + -
1058C VAL* 4.1 18.6 - - + -
1060C LEU* 4.0 15.0 - - + +
1063C PHE* 3.4 35.0 - - + -
1077C LEU* 6.0 2.7 - - + -
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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