Contacts of the strand formed by residues 1076 - 1081 (chain C) in PDB entry 1I7M
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 ARG1076 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1071C PHE* 4.1 10.2 - - - +
1073C SER* 2.7 53.5 + - - +
1075C ARG* 1.3 78.3 - - - +
1077C PHE* 1.3 62.2 + - - +
1078C ILE* 3.5 30.1 - - + +
1174C ASP* 5.4 2.3 + - - -
1237C GLY 4.7 2.0 + - - -
1239C TYR* 3.8 9.7 - - - -
1258C ASN* 3.5 26.3 - - - +
1015D GLU* 3.9 16.8 - - + -
1016D VAL 3.5 4.7 - - - +
1017D TRP* 3.7 50.5 - - + +
1032D LEU* 3.3 6.2 - - - +
1060D GLN* 2.6 31.1 + - - +
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Residues in contact with PHE1077 (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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1070C MSE 3.7 34.1 - - + -
1071C PHE 3.5 12.1 - - - -
1072C VAL* 4.1 9.4 - - + -
1076C ARG* 1.3 75.1 - - - +
1078C ILE* 1.3 64.4 + - - +
1079C LEU* 3.6 38.6 - - + -
1094C LEU* 3.5 42.4 - - + -
1014D LEU* 3.6 5.3 - - + +
1015D GLU* 3.1 7.6 - - - +
1016D VAL* 3.0 39.5 + - + +
1018D PHE* 4.3 7.0 - - + -
1032D LEU* 3.7 15.7 - - + -
1040D TRP* 3.8 21.3 - + - -
1043D LEU* 5.6 1.1 - - + -
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Residues in contact with ILE1078 (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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1070C MSE 3.1 6.1 - - - +
1071C PHE* 2.6 58.5 + - + -
1076C ARG* 3.5 26.9 - - - +
1077C PHE* 1.3 83.1 - - - +
1079C LEU* 1.3 64.7 + - - +
1080C LYS* 4.8 4.3 - - + +
1239C TYR* 3.5 35.0 - - + +
1256C GLU* 4.1 7.0 - - - +
1013D LEU* 3.8 25.8 - - + -
1014D LEU 3.2 3.6 - - - +
1015D GLU* 3.6 22.2 - - + +
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Residues in contact with LEU1079 (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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1069C SER 3.6 2.9 - - - +
1070C MSE 3.7 17.9 - - + -
1077C PHE* 3.6 28.6 - - + -
1078C ILE* 1.3 73.3 - - - +
1080C LYS* 1.3 63.2 + - - +
1081C THR* 4.4 7.9 - - + -
1087C LEU* 3.6 36.1 - - + +
1090C ALA* 4.9 7.4 - - + -
1014D LEU* 3.0 33.7 + - + +
1043D LEU* 4.5 20.0 - - + -
1044D LEU* 4.4 7.6 - - + -
1047D VAL* 6.1 1.6 - - + -
1065D LEU* 3.7 27.6 - - + -
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Residues in contact with LYS1080 (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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1068C PYR 2.9 30.1 - - + +
1069C SER* 2.6 27.9 + - - +
1078C ILE* 4.2 3.6 - - + -
1079C LEU* 1.3 74.3 - - - +
1081C THR* 1.3 68.4 + - - +
1178C GLU* 3.7 15.7 + - - +
1241C THR* 5.4 5.8 + - + -
1243C HIS* 4.7 9.6 - - + +
1254C SER* 4.1 11.7 + - - -
1255C PHE 5.0 0.6 - - - +
1256C GLU* 2.7 43.0 + - - +
1011D GLU* 3.0 39.1 + - + +
1012D LYS 3.5 10.3 - - - +
1013D LEU* 4.0 13.9 - - + -
1065D LEU* 3.8 1.7 - - - +
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Residues in contact with THR1081 (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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1068C PYR 3.7 8.1 - - - -
1079C LEU* 4.4 16.8 - - + -
1080C LYS* 1.3 80.0 - - - +
1082C CYS* 1.3 62.0 + - - +
1085C THR* 3.5 26.1 + - - +
1087C LEU* 3.5 36.4 - - + +
1011D GLU* 3.1 3.8 - - - -
1012D LYS* 2.9 36.8 + - - +
1044D LEU* 5.8 0.9 - - + -
1047D VAL* 5.9 3.6 - - + -
1049D CYS* 5.2 8.5 - - - -
1065D LEU* 4.5 7.2 - - + -
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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