Contacts of the helix formed by residues 113 - 120 (chain 6) in PDB entry 2X17
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 ASP 113 (chain 6).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1021 TYR* 5.3 0.9 + - - -
26 LEU* 3.5 16.6 - - - +
36 SER* 5.1 3.6 + - - -
66 MET* 3.6 14.2 - - + +
646 ARG* 4.2 8.8 + - - -
1086 ALA* 2.9 20.7 + - - +
1116 GLU* 3.1 9.3 - - + +
1126 LYS* 1.3 73.5 - - - +
1146 TYR* 1.3 56.5 + - - +
1156 SER* 3.6 10.6 + - - -
1166 THR* 2.7 37.6 + - - +
1176 ARG* 3.1 26.8 + - - +
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Residues in contact with TYR 114 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1021 TYR* 3.6 56.4 - + + -
1051 ALA* 4.3 8.5 - - + -
1061 ALA* 3.5 20.1 - - - +
1091 GLU* 3.3 35.7 + - - -
1171 ARG* 3.5 21.9 + - - +
1241 ILE* 3.4 14.2 - - + +
1126 LYS* 3.0 53.5 + - + +
1136 ASP* 1.3 70.3 + - - +
1156 SER* 1.3 59.5 + - - +
1176 ARG* 3.7 8.0 - - + +
1186 ALA* 2.8 32.1 + - - +
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Residues in contact with SER 115 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1021 TYR* 2.6 31.0 + - - -
1241 ILE* 3.7 12.6 + - - +
1251 ASN* 4.8 1.9 - - - +
1281 VAL* 3.8 17.3 - - - +
606 TYR* 3.1 11.0 + - - -
646 ARG* 3.4 30.7 + - - -
1136 ASP* 3.3 3.1 + - - -
1146 TYR* 1.3 78.9 - - - +
1166 THR* 1.3 57.6 + - - +
1186 ALA* 3.6 2.4 + - - +
1196 PHE* 3.0 24.4 + - - +
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Residues in contact with THR 116 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26 LEU* 3.5 8.8 - - - +
66 MET* 3.8 23.1 - - + -
106 LEU* 4.1 17.3 - - + -
606 TYR* 2.7 24.8 + - + -
1086 ALA* 4.3 2.9 - - + -
1136 ASP* 2.7 33.6 + - - -
1146 TYR 3.4 0.2 - - - -
1156 SER* 1.3 73.6 - - - +
1176 ARG* 1.3 60.4 + - - +
1196 PHE* 3.3 2.0 + - + +
1206 LEU* 2.9 45.8 + - + +
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Residues in contact with ARG 117 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1171 ARG* 5.1 10.5 - - - +
1211 GLU* 4.7 1.4 + - - +
1145 TYR* 3.6 23.0 + - - +
1175 ARG* 5.1 11.7 - - - +
1185 ALA* 5.8 0.6 - - - +
1056 ALA* 3.7 30.1 - - - +
1086 ALA* 3.9 9.4 - - + +
1096 GLU* 3.2 30.4 + - + -
1136 ASP 3.1 18.9 + - - +
1146 TYR* 3.7 11.0 - - + +
1156 SER 3.4 0.2 - - - -
1166 THR* 1.3 77.6 - - - +
1186 ALA* 1.3 58.9 + - - +
1206 LEU* 3.7 3.5 + - - +
1216 GLU* 3.0 34.5 + - - +
1246 ILE* 3.6 19.9 - - - +
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Residues in contact with ALA 118 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1171 ARG* 5.9 0.2 - - - +
1211 GLU* 3.6 30.6 - - - +
1241 ILE* 3.8 16.2 - - + -
1251 ASN* 3.4 27.7 + - - +
1146 TYR 2.8 18.4 + - - +
1156 SER 3.9 2.2 - - - +
1176 ARG* 1.3 74.7 - - - +
1196 PHE* 1.3 64.6 + - - +
1216 GLU* 3.3 15.4 - - - +
1226 TRP* 4.4 1.4 + - - +
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Residues in contact with PHE 119 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1251 ASN* 4.1 4.7 + - - +
106 LEU* 4.4 3.1 - - + -
566 ARG* 3.7 16.2 - - + -
576 PHE* 3.6 35.7 - + - -
606 TYR* 3.5 58.6 - + + -
1156 SER 3.0 18.6 + - - +
1166 THR* 3.5 8.7 - - + +
1186 ALA* 1.3 77.9 - - - +
1206 LEU* 1.3 70.0 + - + +
1216 GLU 3.1 2.7 + - - -
1226 TRP* 3.5 19.1 + - + +
1236 PHE* 3.5 30.5 - + - -
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Residues in contact with LEU 120 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106 LEU* 5.2 0.2 - - + -
576 PHE* 4.2 21.5 - - + -
1016 ILE* 4.3 15.4 - - + +
1046 LEU* 3.5 59.7 - - + +
1056 ALA* 3.8 8.5 - - + +
1086 ALA* 4.6 2.0 - - + -
1166 THR* 2.9 34.3 + - + +
1176 ARG* 4.1 9.9 - - - +
1186 ALA 3.4 0.4 - - - -
1196 PHE* 1.3 81.9 - - + +
1216 GLU* 1.3 62.7 + - - +
1226 TRP 3.2 0.7 - - - -
1236 PHE* 3.1 18.8 + - + +
1246 ILE* 3.1 21.2 + - + +
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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