Contacts of the strand formed by residues 1120 - 1124 (chain B) in PDB entry 2RFI
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 PHE1120 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1057B GLY 4.9 3.6 + - - -
1088B VAL* 3.7 19.0 - - + +
1089B VAL* 3.8 42.2 - - + -
1092B GLY* 3.6 34.5 - - - -
1093B LEU* 4.0 5.6 - - - -
1094B ARG* 5.4 5.3 + - + +
1095B ALA* 5.2 6.2 + - - +
1118B GLY 3.9 0.4 + - - -
1119B THR* 1.3 83.0 - - - +
1121B VAL* 1.3 62.5 + - - +
1122B CYS* 3.4 36.8 - - - -
1123B GLU* 3.8 8.3 - - + -
1194B ALA* 3.7 19.1 - - + -
1195B PHE 3.7 6.7 - - - -
1196B PHE* 3.5 25.2 - + + -
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Residues in contact with VAL1121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1093B LEU* 4.1 21.0 - - - +
1094B ARG 4.7 0.5 + - - -
1095B ALA* 4.7 9.3 - - + +
1097B LEU* 4.2 16.1 - - + +
1115B ILE* 4.2 29.4 - - + -
1119B THR* 3.5 15.0 - - + +
1120B PHE* 1.3 77.9 - - - +
1122B CYS* 1.3 68.2 + - - +
1176B LEU* 3.6 25.4 - - + -
1195B PHE 2.8 15.1 + - - +
1197B SER* 4.1 4.3 - - - +
1201B ILE* 5.0 0.4 - - + -
1207B LEU* 3.8 28.3 - - + -
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Residues in contact with CYS1122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1093B LEU* 4.6 9.2 - - + -
1097B LEU* 4.4 11.2 - - + -
1120B PHE* 3.4 14.1 - - - -
1121B VAL* 1.3 93.3 - - - +
1123B GLU* 1.3 56.5 + - - +
1163B ASN* 5.0 1.1 - - - +
1164B VAL* 4.4 15.5 - - + -
1165B SER* 3.1 24.7 - - - +
1168B ILE* 3.8 22.4 - - - -
1176B LEU* 5.2 0.2 - - - -
1195B PHE* 2.8 41.7 + - - -
1207B LEU* 4.9 0.2 - - - -
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Residues in contact with GLU1123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1012B GLN* 6.0 0.6 - - - -
1013B ASN* 3.7 15.8 + - - -
1089B VAL* 4.5 10.3 - - + +
1120B PHE* 3.8 11.7 - - + -
1122B CYS* 1.3 73.8 - - - +
1124B TYR* 1.3 59.3 + - - +
1125B VAL* 3.3 21.0 + - + +
1163B ASN* 2.8 20.4 + - - +
1165B SER* 2.6 22.4 + - - -
1192B ARG* 2.8 55.3 + - - +
1193B ILE 3.1 20.4 - - - +
1194B ALA* 4.4 1.6 - - - +
1195B PHE* 4.4 0.4 - - - -
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Residues in contact with TYR1124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1013B ASN* 3.8 1.2 - - - +
1123B GLU* 1.3 74.3 - - - +
1125B VAL* 1.3 60.0 + - - +
1142B TYR* 2.7 27.9 + - - -
1144B PHE* 3.6 36.8 - + + -
1156B ILE* 3.4 42.1 - - + +
1158B ALA* 3.5 17.4 - - + +
1165B SER* 3.8 27.1 - - - -
1166B ARG* 4.3 2.2 - - - -
1193B ILE* 2.8 29.8 + - + +
1195B PHE* 3.7 24.7 - + + -
7Q MLY 3.2 38.9 + - - -
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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