Contacts of the strand formed by residues 1143 - 1147 (chain C) in PDB entry 5GLJ
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 ARG1143 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1117A LEU* 2.8 47.7 + - - +
1119A LEU* 4.2 7.2 - - - +
1153A GLU* 2.8 30.1 + - - +
1089C ARG* 4.3 4.2 - - - +
1119C LEU* 2.9 47.7 + - + +
1121C ILE 3.7 8.5 - - - +
1122C PHE* 3.8 23.7 - - + -
1123C ILE* 5.4 0.2 - - - -
1141C GLY 3.6 0.4 + - - -
1142C ASP* 1.3 71.3 - - - +
1144C LEU* 1.3 63.6 + - - +
1145C ILE* 3.6 14.8 + - + +
1175C ILE* 3.1 9.9 - - - +
1176C SER* 3.0 44.3 + - - +
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Residues in contact with LEU1144 (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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1106C PHE* 4.4 7.4 - - + -
1108C ILE* 4.2 22.2 - - + -
1119C LEU* 4.3 4.3 - - - +
1121C ILE* 3.0 29.1 + - + +
1123C ILE* 4.3 13.5 - - + -
1142C ASP 3.8 2.0 + - - -
1143C ARG* 1.3 71.3 - - - +
1145C ILE* 1.3 62.0 + - - +
1146C SER 3.7 21.1 - - - +
1147C VAL* 4.3 11.4 - - + -
1152C LEU* 3.6 35.4 - - + +
1164C LEU* 4.4 10.5 - - + -
1173C LEU* 3.9 18.4 - - + -
1174C VAL 3.9 7.9 - - - +
1175C ILE* 3.9 13.7 - - + -
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Residues in contact with ILE1145 (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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1091A ILE* 4.1 10.3 - - + -
1119A LEU* 5.3 1.8 - - + -
1145A ILE* 4.1 34.5 - - + -
1153A GLU* 4.6 5.8 - - - +
1091C ILE* 4.0 13.7 - - + -
1119C LEU* 3.9 25.0 - - + +
1143C ARG* 4.1 18.2 - - + +
1144C LEU* 1.3 77.4 - - - +
1146C SER* 1.3 61.3 + - - +
1151C SER* 3.8 2.8 + - - -
1152C LEU* 2.9 24.9 + - - +
1153C GLU* 6.2 0.2 - - + -
1174C VAL* 2.8 24.4 + - + +
1175C ILE 4.2 1.8 - - - -
1176C SER* 3.9 31.4 - - - +
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Residues in contact with SER1146 (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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1091A ILE* 3.3 28.3 - - - +
1144C LEU* 3.7 7.3 - - - +
1145C ILE* 1.3 82.3 - - - +
1147C VAL* 1.3 67.8 + - - +
1148C ASN 3.3 13.9 + - - -
1150C VAL 3.3 9.2 - - - -
1152C LEU* 4.4 2.5 - - - +
1173C LEU* 3.5 6.9 - - - -
1174C VAL* 3.2 43.3 + - - +
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Residues in contact with VAL1147 (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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1144C LEU* 4.3 11.9 - - + -
1146C SER* 1.3 77.9 - - - +
1148C ASN* 1.3 71.7 + - - +
1150C VAL* 2.9 29.4 + - - +
1152C LEU* 4.5 8.5 - - + -
1160C ALA 5.6 0.2 - - - +
1163C ILE* 3.8 27.8 - - + +
1164C LEU* 3.6 32.8 - - + -
1167C ALA* 4.0 26.5 - - + -
1171C VAL* 4.2 11.4 - - + -
1172C THR 3.9 1.8 - - - -
1173C LEU* 4.3 3.4 - - + -
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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