Contacts of the strand formed by residues 1158 - 1163 (chain N) in PDB entry 2JA7
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 PHE1158 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2M VAL* 3.2 9.7 - - - +
3M GLY* 5.1 9.9 - - - -
75M ASN* 5.4 2.2 - - - -
76M GLU* 4.2 31.4 - - - -
78M PRO* 4.4 12.6 - - + -
1116N ARG* 3.9 24.5 - - - -
1152N MET* 4.1 1.2 - - - +
1157N ALA* 1.3 76.5 - - - +
1159N ARG* 1.3 78.7 + - - +
1160N VAL* 3.9 22.5 + - + -
1194N ILE 3.7 0.3 - - - +
1195N HIS* 3.4 5.5 - - - -
1196N ILE* 3.0 39.2 + - - +
1198N TYR* 3.7 30.3 - + + +
1201N LYS* 3.8 31.0 - - + -
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Residues in contact with ARG1159 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2M VAL* 3.5 19.7 + - - +
3M GLY* 4.5 5.7 - - - -
4M GLN 3.5 9.3 + - - +
5M GLN 2.7 28.9 + - - -
7M SER* 4.2 5.7 - - - +
76M GLU* 2.9 39.8 + - - +
78M PRO* 6.1 0.2 - - - +
1158N PHE* 1.3 94.0 - - - +
1160N VAL* 1.3 65.3 + - - +
1161N HIS* 3.9 12.2 + - - -
1175N LEU* 3.7 13.2 - - - +
1193N GLN* 3.1 40.0 - - + +
1194N ILE 3.4 11.7 - - - +
1195N HIS* 3.7 17.5 - - + +
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Residues in contact with VAL1160 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78M PRO* 4.3 28.5 - - + -
1158N PHE* 3.9 21.5 - - + -
1159N ARG* 1.3 81.5 - - - +
1161N HIS* 1.3 76.4 + - - +
1162N ILE* 5.8 0.2 - - + -
1169N MET* 3.5 37.2 - - + +
1193N GLN* 3.5 3.8 - - - -
1194N ILE* 3.0 36.7 + - + +
1196N ILE* 4.4 21.3 - - + -
1201N LYS* 4.9 1.3 - - + -
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Residues in contact with HIS1161 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7M SER* 3.6 27.6 - - - -
9M ALA* 3.7 7.0 - - + +
76M GLU* 4.9 4.7 - - - -
1159N ARG* 3.9 10.6 + - - -
1160N VAL* 1.3 83.1 - - - +
1162N ILE* 1.3 65.4 + - - +
1168N LEU 3.7 8.3 - - - +
1169N MET* 3.8 13.5 - - - +
1171N VAL* 3.7 27.9 - - + +
1173N ALA* 3.1 25.6 - - + -
1175N LEU* 3.0 22.5 - - + +
1180N PHE* 3.7 15.5 - + - -
1191N ILE* 4.7 0.2 - - + -
1192N TYR 3.4 14.4 + - - +
1193N GLN* 3.7 13.5 - - + +
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Residues in contact with ILE1162 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14M VAL* 5.1 0.9 - - + -
1160N VAL* 5.8 0.4 - - + -
1161N HIS* 1.3 78.1 - - - +
1163N CYS* 1.3 80.1 + - - +
1164N GLY 3.9 0.2 - - - -
1167N GLY 4.0 0.9 - - - -
1168N LEU 3.1 26.7 - - - +
1169N MET* 6.4 1.3 - - - -
1171N VAL* 2.9 15.6 - - - +
1191N ILE* 3.5 7.4 - - - +
1192N TYR* 2.9 32.0 + - + +
1194N ILE* 3.4 51.6 - - + -
1216N LEU* 3.8 29.6 - - + +
1218N THR* 4.5 11.4 - - + -
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Residues in contact with CYS1163 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1162N ILE* 1.3 88.2 - - - +
1164N GLY* 1.3 62.2 - - - +
1165N ILE* 2.9 19.5 + - - -
1166N CYS* 3.0 42.6 - - - +
1167N GLY* 3.9 2.6 - - - -
1168N LEU 3.6 3.0 + - - +
1170N THR* 5.0 0.9 - - - +
1171N VAL* 3.5 5.5 - - + +
1182N CYS* 4.0 8.7 - - + -
1185N CYS* 3.7 2.0 - - - -
1187N ASN* 4.1 11.4 - - - -
1190N ASP 4.1 3.1 - - - -
1191N ILE* 4.8 1.1 - - - -
1192N TYR* 5.2 0.2 - - - -
1216N LEU 4.6 2.3 - - - +
1217N TYR* 5.3 0.2 - - - -
2457N ZN 2.5 35.2 - - - -
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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