Contacts of the strand formed by residues 1094 - 1102 (chain C) in PDB entry 4UVL
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 ARG1094 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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986C GLY* 2.9 24.0 + - - -
1069C ASN* 3.0 30.2 + - - +
1072C VAL* 4.2 10.3 - - + +
1073C TYR* 3.6 39.6 + - + +
1087C ARG 2.9 25.2 + - - -
1089C CYS* 3.2 32.9 + - - +
1092C CYS 4.0 6.0 + - - +
1093C HIS* 1.3 74.6 - - - +
1095C GLN* 1.3 65.4 + - - +
1154C THR* 3.3 5.5 - - - +
1155C TYR* 2.7 60.7 + - + +
1157C ILE* 3.5 20.1 - - - +
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Residues in contact with GLN1095 (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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980A ARG* 5.2 5.9 - - - +
1131A VAL* 4.6 16.5 - - - +
998C GLN* 4.9 2.2 + - - -
1033C SER 4.8 1.0 + - - +
1036C VAL* 4.1 23.6 - - + +
1037C ASN 5.9 0.5 + - - -
1072C VAL* 3.7 22.3 - - - +
1093C HIS* 5.5 1.3 - - + +
1094C ARG* 1.3 80.2 - - - +
1096C LEU* 1.3 59.0 + - - +
1152C LEU* 3.8 35.0 - - + +
1153C ILE 3.1 7.2 - - - +
1154C THR* 3.0 30.1 + - + +
1155C TYR* 3.8 4.3 - - - -
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Residues in contact with LEU1096 (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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972C MET* 3.7 30.3 - - + -
992C TYR* 4.9 1.6 - - - +
1030C PHE* 4.3 11.7 - - + -
1031C HIS 3.8 3.6 - - - +
1032C GLY* 3.6 17.5 - - - -
1036C VAL* 5.1 1.3 - - - -
1065C SER* 3.8 18.8 - - - +
1068C SER* 3.6 34.3 - - - -
1069C ASN 3.8 0.9 - - - +
1072C VAL* 3.6 10.5 - - + -
1095C GLN* 1.3 71.2 - - - +
1097C LEU* 1.3 68.4 + - - +
1152C LEU* 3.8 5.4 - - - +
1153C ILE* 2.9 37.1 + - + +
1155C TYR* 3.5 20.6 - - + +
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Residues in contact with LEU1097 (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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1030C PHE* 3.3 8.9 - - - +
1031C HIS* 2.9 39.9 + - + +
1036C VAL* 3.9 12.1 - - + -
1039C ILE* 3.7 41.1 - - + -
1040C ILE* 3.7 23.8 - - + -
1044C PHE* 4.1 10.1 - - + -
1096C LEU* 1.3 75.4 - - - +
1098C PHE* 1.3 58.9 + - - +
1099C CYS* 3.5 13.2 - - - -
1149C PRO* 3.8 14.1 - - + +
1151C TYR 3.2 12.8 - - - +
1152C LEU* 3.8 19.7 - - + -
1153C ILE* 4.9 0.9 - - - -
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Residues in contact with PHE1098 (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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968C VAL* 4.2 22.0 - - + -
971C GLU* 3.7 26.9 - - + -
1028C MET* 3.4 48.9 - - + -
1029C LEU 3.7 9.9 - - - -
1030C PHE* 3.5 34.8 - + + -
1097C LEU* 1.3 72.7 - - - +
1099C CYS* 1.3 60.0 + - - +
1150C GLU* 3.4 3.3 + - - +
1151C TYR* 2.9 59.5 + + + -
1153C ILE* 3.9 18.6 - - + +
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Residues in contact with CYS1099 (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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1027C ARG 3.4 0.5 - - - +
1028C MET* 3.2 11.4 - - - -
1029C LEU 2.8 36.5 + - - +
1031C HIS* 4.0 5.4 - - - -
1044C PHE* 3.8 24.2 - - + -
1061C PHE* 3.8 19.7 - - + -
1097C LEU* 3.5 30.7 - - - -
1098C PHE* 1.3 73.0 - - - +
1100C ARG* 1.3 61.6 + - - +
1101C VAL* 3.7 6.0 + - + +
1148C TYR 3.3 12.1 - - - +
1149C PRO* 3.9 8.3 - - - -
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Residues in contact with ARG1100 (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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1006C TRP* 3.8 18.4 - - - -
1009C TYR* 3.5 18.3 - - + +
1013C ARG* 4.2 4.2 - - - +
1026C GLU* 2.9 51.4 + - + +
1027C ARG 3.5 3.4 - - - -
1028C MET* 3.7 20.8 - - - +
1099C CYS* 1.3 72.1 - - - +
1101C VAL* 1.3 58.1 + - - +
1147C ALA* 3.3 3.6 - - - -
1148C TYR* 2.8 38.6 + - + +
1150C GLU* 2.9 44.0 + - - +
2166C PEG 5.6 0.4 + - - -
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Residues in contact with VAL1101 (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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1009C TYR* 3.7 3.4 - - - -
1025C ASN 3.8 0.3 - - - +
1026C GLU* 3.4 2.4 - - - -
1027C ARG* 2.8 38.1 + - - +
1029C LEU* 4.0 18.4 - - + -
1061C PHE* 3.8 44.9 - - + -
1099C CYS* 3.8 12.8 - - + +
1100C ARG* 1.3 78.7 - - - +
1102C THR* 1.3 61.8 + - - +
1103C LEU* 3.6 16.8 + - + +
1139C TYR* 5.7 0.4 - - + -
1141C ILE* 4.0 23.8 - - + -
1146C GLN 3.5 9.0 - - - +
1147C ALA* 4.3 1.1 - - + -
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Residues in contact with THR1102 (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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1009C TYR* 2.8 28.3 + - - -
1013C ARG* 3.5 22.9 - - - +
1016C VAL* 3.6 36.6 - - + -
1024C ALA* 3.4 23.0 - - + +
1025C ASN 4.3 0.7 - - - -
1026C GLU* 4.2 3.6 + - - +
1101C VAL* 1.3 69.8 - - - +
1103C LEU* 1.3 58.1 + - - +
1141C ILE* 3.9 5.2 - - - +
1146C GLN* 2.9 45.5 + - + +
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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