Contacts of the strand formed by residues 988 - 995 (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 MET 988 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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982C ILE* 4.6 1.1 - - - -
984C LYS 5.7 0.7 - - - +
986C ASN 3.8 0.2 + - - -
987C GLU* 1.3 76.7 - - - +
989C LEU* 1.3 74.5 + - - +
990C VAL* 3.6 13.7 + - + -
1011C ILE* 2.9 39.7 + - + +
1060C LEU* 3.6 26.0 - - + -
1063C PHE* 3.6 44.2 - - + -
1064C GLU* 4.0 21.8 - - - +
1074C ARG* 4.5 18.4 - - - +
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Residues in contact with LEU 989 (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* 4.1 13.2 - - - +
979C GLN* 3.7 55.6 - - + +
982C ILE* 3.9 23.4 - - + +
988C MET* 1.3 82.4 - - - +
990C VAL* 1.3 59.4 + - - +
1008C LEU* 5.1 14.8 - - + +
1009C LEU 3.5 2.2 - - - +
1010C ARG* 3.8 19.7 - - + +
1074C ARG* 5.6 2.1 + - - -
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Residues in contact with VAL 990 (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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988C MET* 3.6 6.7 + - + -
989C LEU* 1.3 74.4 - - - +
991C THR* 1.3 72.9 + - - +
992C VAL* 3.6 7.3 - - + +
1008C LEU* 3.5 7.3 - - - -
1009C LEU* 2.9 55.5 + - + +
1011C ILE* 3.6 26.7 - - + -
1063C PHE* 4.4 29.4 - - + -
1075C PRO 4.6 8.3 - - - +
1077C LEU* 4.5 12.6 - - + +
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Residues in contact with THR 991 (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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948C LYS* 5.9 0.2 - - - +
949C ILE* 3.6 36.1 + - - +
990C VAL* 1.3 75.5 - - - +
992C VAL* 1.3 63.8 + - - +
993C ALA* 5.7 1.0 - - - +
1008C LEU* 3.7 18.1 - - - +
1074C ARG* 5.0 6.5 - - + +
1075C PRO 4.1 10.1 - - - +
1076C TRP* 3.4 22.3 - - + +
1077C LEU 3.0 23.4 + - - -
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Residues in contact with VAL 992 (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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990C VAL* 3.6 17.5 - - + +
991C THR* 1.3 82.8 + - - +
993C ALA* 1.3 63.6 + - - +
1006C PRO* 3.2 8.0 - - - +
1007C PHE* 2.9 69.7 + - + +
1009C LEU* 3.7 22.2 - - + -
1024C ILE* 5.1 0.4 - - + -
1076C TRP* 5.0 0.2 - - - -
1077C LEU* 3.6 33.2 - - + +
1079C LEU* 4.3 12.8 - - + -
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Residues in contact with ALA 993 (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 3.8 20.2 - - - +
948C LYS* 4.3 11.0 - - + -
949C ILE 5.5 0.4 - - - +
991C THR* 5.7 0.7 - - - +
992C VAL* 1.3 77.5 - - - +
994C HIS* 1.3 71.3 + - - +
1006C PRO* 4.3 6.1 - - + -
1076C TRP* 3.6 24.0 - - + -
1077C LEU 3.0 10.7 + - - +
1078C GLY* 3.6 1.6 - - - -
1079C LEU* 3.1 26.4 + - - +
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Residues in contact with HIS 994 (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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993C ALA* 1.3 84.2 + - - +
995C PHE* 1.3 67.0 + - - +
1002C THR* 3.3 21.0 - - - +
1003C PHE* 3.2 41.4 + + + +
1004C GLY* 4.4 9.0 - - - -
1005C ILE 4.2 14.7 + - - -
1006C PRO* 5.5 0.2 - - - +
1007C PHE* 4.1 18.2 - + - -
1028C LEU* 4.1 20.5 - - + +
1076C TRP* 4.9 0.3 - - - -
1079C LEU* 3.7 26.7 - - + +
1081C HIS* 3.2 31.2 + + + -
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Residues in contact with PHE 995 (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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993C ALA 4.5 0.2 - - - -
994C HIS* 1.3 80.6 - - - +
996C HIS* 1.3 56.9 + - - +
997C LYS 3.1 20.9 - - - -
998C GLU 3.0 21.3 - - - +
999C VAL* 3.7 23.8 - - + -
1001C GLY 3.1 19.7 - - - +
1002C THR* 3.8 7.4 - - + +
1003C PHE* 3.4 12.2 - - - -
1039C LYS 4.8 0.9 - - - -
1041C ALA* 4.4 13.2 - - + -
1043C VAL* 5.4 0.2 - - + -
1048C HIS* 5.7 1.1 - + - -
1050C TYR* 4.2 11.9 - + - -
1076C TRP* 4.8 6.3 - + + -
1078C GLY* 3.2 17.9 - - - -
1079C LEU 3.0 57.3 + - - +
1080C ASP* 2.8 33.1 - - + +
1081C HIS 4.2 0.2 + - - -
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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