Contacts of the strand formed by residues 1117 - 1124 (chain B) in PDB entry 1CJY
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 LYS1117 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1023B VAL* 5.3 6.2 - - - +
1115B GLY 4.0 2.8 + - - +
1116B GLU* 1.3 78.5 - - - +
1118B LYS* 1.3 67.7 + - - +
1119B GLU* 5.9 0.6 - - - +
1133B GLU* 3.5 28.7 + - - +
1134B MET 3.2 6.1 - - - +
1135B SER* 3.2 23.3 + - - +
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Residues in contact with LYS1118 (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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1107B PHE* 4.8 7.9 - - - -
1111B SER* 4.0 17.6 + - - -
1112B MET* 4.1 21.8 - - + -
1116B GLU* 2.8 29.3 + - + +
1117B LYS* 1.3 80.5 - - - +
1119B GLU* 1.3 65.1 + - - +
1120B VAL* 3.9 18.2 + - + -
1132B LEU 3.9 0.2 - - - +
1133B GLU* 4.2 1.8 - - - -
1134B MET* 2.8 38.4 + - + +
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Residues in contact with GLU1119 (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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1025B LEU* 3.2 27.0 - - + +
1026B ARG* 4.6 8.5 + - - -
1117B LYS* 5.9 0.4 - - - +
1118B LYS* 1.3 79.4 - - - +
1120B VAL* 1.3 63.9 + - - +
1121B PRO* 4.1 5.1 - - - +
1131B VAL* 3.8 15.1 - - + +
1132B LEU 3.2 5.6 - - - +
1133B GLU* 4.0 16.5 - - + +
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Residues in contact with VAL1120 (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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1107B PHE* 3.8 28.0 - - + -
1118B LYS* 4.2 15.3 - - + +
1119B GLU* 1.3 79.8 - - - +
1121B PRO* 1.3 73.0 - - + +
1122B PHE* 3.3 37.3 - - + -
1131B VAL* 3.6 2.9 - - - -
1132B LEU 2.7 32.4 + - - +
1134B MET* 4.0 15.3 - - + -
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Residues in contact with PRO1121 (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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1119B GLU 4.1 4.9 - - - +
1120B VAL* 1.3 93.9 - - + +
1122B PHE* 1.3 65.5 + - - +
1123B ILE* 5.7 0.8 - - - +
1129B GLU* 6.2 2.7 - - + -
1130B MET 3.4 8.1 - - - +
1131B VAL* 4.5 10.8 - - + -
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Residues in contact with PHE1122 (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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1089B ILE* 3.6 22.7 - - + -
1105B ALA* 3.6 20.4 - - + -
1106B THR 3.1 26.0 - - - -
1107B PHE* 4.1 4.0 - + - -
1120B VAL* 3.3 44.2 - - + -
1121B PRO* 1.3 76.7 - - - +
1123B ILE* 1.3 61.3 + - - +
1124B PHE* 3.8 21.8 - + + -
1128B THR 3.9 0.2 - - - +
1129B GLU* 3.5 3.6 - - - +
1130B MET* 2.7 48.7 + - + +
1132B LEU* 4.2 20.2 - - + -
1134B MET* 4.1 11.0 - - + -
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Residues in contact with ILE1123 (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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1121B PRO 5.7 0.7 - - - +
1122B PHE* 1.3 75.1 - - - +
1124B PHE* 1.3 65.6 + - - +
1125B ASN 4.2 0.9 + - - -
1126B GLN* 3.3 43.2 + - - +
1127B VAL 3.3 8.1 - - - +
1128B THR 2.9 29.2 - - - +
1129B GLU* 4.4 5.2 - - + +
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Residues in contact with PHE1124 (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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1089B ILE* 4.3 7.4 - - + -
1091B LEU* 4.3 19.3 - - + -
1103B GLY* 3.4 42.6 - - - -
1104B THR* 3.7 6.7 - - - -
1105B ALA* 3.8 27.1 - - + -
1122B PHE* 3.8 16.2 - - + -
1123B ILE* 1.3 74.1 - - - +
1125B ASN* 1.3 76.6 + - - +
1126B GLN 3.1 3.3 + - - -
1127B VAL 3.3 0.2 + - - -
1128B THR* 2.9 48.5 + - + +
1130B MET* 3.4 48.9 - - + -
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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