Contacts of the strand formed by residues 1112 - 1125 (chain F) in PDB entry 1NYE
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 GLY1112 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1108F LYS* 3.4 3.6 - - - +
1109F VAL 2.5 43.4 + - - +
1110F ASP* 4.2 1.3 - - - +
1111F ALA* 1.3 81.2 - - - +
1113F PHE* 1.3 61.9 + - - -
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Residues in contact with PHE1113 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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821E MET 5.5 2.0 - - - -
823E ILE* 5.3 9.2 - - + -
944E GLY 4.8 6.1 - - - +
946E PRO* 3.9 22.5 - - + +
949E GLN* 5.1 4.3 + - - +
1106F LEU* 3.7 31.6 - - + -
1107F ASP* 3.2 7.9 - - - -
1108F LYS* 3.3 41.3 - - + -
1109F VAL* 4.7 0.7 - - - -
1112F GLY* 1.3 77.8 - - - -
1114F ALA* 1.3 63.4 + - - +
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Residues in contact with ALA1114 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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946E PRO* 4.5 5.8 - - - -
949E GLN* 5.2 13.2 - - + +
950E VAL* 6.1 0.2 - - + -
1106F LEU* 3.7 7.7 - - - +
1107F ASP 2.9 26.0 + - - -
1109F VAL* 4.3 18.6 - - + -
1113F PHE* 1.3 77.6 - - - +
1115F ILE* 1.3 60.9 + - - +
1116F THR* 2.9 17.4 + - + +
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Residues in contact with ILE1115 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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946E PRO* 4.4 7.8 - - + +
947E VAL* 5.0 0.2 - - - -
950E VAL* 3.3 37.9 - - + +
1069F GLU* 3.4 30.5 - - + +
1072F ILE* 4.0 26.9 - - + -
1104F VAL* 3.6 30.1 - - + -
1105F SER 3.3 7.4 - - - +
1106F LEU* 3.9 7.6 - - + +
1114F ALA* 1.3 71.5 - - - +
1116F THR* 1.3 57.6 + - - +
1117F LYS 4.3 6.5 - - - +
1118F ILE* 4.4 9.2 - - + -
1153F ALA* 3.4 21.5 - - + +
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Residues in contact with THR1116 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1105F SER* 2.8 15.7 + - - -
1107F ASP* 2.9 34.6 + - + +
1109F VAL* 3.9 17.0 - - + -
1114F ALA* 2.9 18.9 + - + +
1115F ILE* 1.3 74.1 - - - +
1117F LYS* 1.3 66.3 + - - +
1153F ALA* 3.8 5.8 - - - +
1154F GLU* 3.2 19.4 + - - +
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Residues in contact with LYS1117 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1103F ASP 3.5 1.3 - - - +
1104F VAL* 3.5 1.9 - - - +
1105F SER* 2.6 44.9 + - - +
1115F ILE* 3.5 2.6 - - - +
1116F THR* 1.3 91.0 + - - +
1118F ILE* 1.3 71.1 + - - +
1119F ALA* 4.5 9.4 - - + +
1153F ALA* 3.9 1.7 - - - +
1154F GLU* 3.3 32.9 + - + +
1156F THR* 3.6 34.7 - - + +
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Residues in contact with ILE1118 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1072F ILE* 4.2 19.7 - - + -
1076F HIS* 3.0 35.7 - - + +
1102F ALA* 4.4 13.9 - - + -
1103F ASP 3.0 8.3 - - - +
1104F VAL* 4.0 18.2 - - + -
1115F ILE* 4.4 10.5 - - + -
1117F LYS* 1.3 80.8 - - - +
1119F ALA* 1.3 67.2 + - - +
1120F LEU* 3.8 1.6 + - + -
1151F LEU* 3.4 34.3 - - + -
1153F ALA* 4.8 4.5 - - + +
1154F GLU 2.9 8.1 + - - +
1155F ILE* 3.4 9.8 - - + +
1156F THR 3.4 18.4 + - - -
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Residues in contact with ALA1119 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1101F THR 3.5 1.6 - - - +
1102F ALA* 3.5 1.9 - - - -
1103F ASP* 2.7 52.6 + - + +
1117F LYS* 4.1 13.4 - - + +
1118F ILE* 1.3 73.0 - - - +
1120F LEU* 1.3 61.7 + - - +
1121F LYS* 3.9 1.7 + - - +
1156F THR* 3.2 20.4 - - - +
1158F ASP* 5.8 1.6 - - - +
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Residues in contact with LEU1120 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1076F HIS* 4.1 36.3 - - + +
1077F ALA* 4.6 10.8 - - + -
1080F PHE* 3.8 40.8 - - + -
1100F THR* 5.4 1.8 - - - +
1101F THR 3.3 4.9 - - - +
1102F ALA* 3.7 28.3 - - + -
1119F ALA* 1.3 74.3 - - - +
1121F LYS* 1.3 59.8 + - - +
1142F LYS* 4.6 5.4 - - + -
1148F SER* 5.0 0.9 - - - +
1155F ILE* 4.3 11.0 - - + -
1156F THR 2.8 15.4 + - - +
1157F LEU* 3.4 11.3 - - + +
1158F ASP* 2.8 28.6 + - - +
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Residues in contact with LYS1121 (chain F).
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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1099F ASP 4.0 0.3 - - - +
1100F THR* 3.3 1.5 - - - -
1101F THR* 2.5 60.8 + - - -
1119F ALA 3.9 1.5 + - - +
1120F LEU* 1.3 73.5 - - - +
1122F SER* 1.3 61.1 + - - +
1123F GLU* 3.5 34.1 + - - +
1158F ASP* 3.0 22.4 - - + +
1159F TYR* 5.5 0.2 - - - -
1160F GLN* 5.2 3.8 + - - +
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Residues in contact with SER1122 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1080F PHE* 4.1 14.8 - - - -
1098F ILE* 4.1 0.2 - - - +
1099F ASP 3.2 5.4 + - - -
1100F THR* 2.8 31.4 - - - +
1120F LEU* 4.2 0.6 - - - -
1121F LYS* 1.3 76.0 - - - +
1123F GLU* 1.3 66.7 + - - +
1124F VAL* 3.4 17.7 - - - +
1138F ILE* 6.2 0.2 - - - -
1157F LEU* 4.7 3.8 - - - +
1158F ASP 2.7 10.3 + - - -
1159F TYR* 2.9 37.3 - - - +
1160F GLN* 2.9 4.3 + - - +
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Residues in contact with GLU1123 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1097F SER* 4.1 1.6 + - - +
1098F ILE* 3.8 1.2 - - - -
1099F ASP* 2.7 49.3 + - + +
1121F LYS* 3.5 23.2 + - - +
1122F SER* 1.3 76.7 + - - +
1124F VAL* 1.3 61.7 + - - +
1160F GLN* 3.4 31.9 - - + +
1162F LYS* 3.8 24.8 + - - +
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Residues in contact with VAL1124 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1084F LEU* 3.7 19.5 - - + -
1088F LEU* 4.8 0.4 - - + -
1097F SER 3.6 2.2 - - - -
1098F ILE* 3.7 22.4 - - + -
1122F SER* 3.4 24.5 - - - +
1123F GLU* 1.3 73.3 - - - +
1125F ALA* 1.3 64.2 + - - +
1126F VAL* 3.5 24.5 - - + -
1134F PHE* 3.7 26.7 - - + -
1138F ILE* 5.0 2.7 - - + -
1159F TYR* 5.2 3.4 - - + -
1160F GLN 2.9 11.5 + - - +
1161F LEU* 3.3 7.4 - - + +
1162F LYS* 2.8 29.1 + - - +
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Residues in contact with ALA1125 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1095F PRO* 3.5 1.6 - - - +
1096F THR* 3.0 39.6 + - - +
1097F SER* 2.9 21.4 + - - +
1124F VAL* 1.3 74.6 - - - +
1126F VAL* 1.3 66.1 + - - +
1162F LYS* 3.9 28.9 - - + +
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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