Contacts of the helix formed by residues 113 - 120 (chain 4) 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 4).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24 LEU* 3.7 17.4 - - - +
34 SER 5.5 0.5 + - - -
64 MET* 3.8 13.5 - - + +
644 ARG* 4.8 4.9 + - - -
1084 ALA* 2.8 25.4 + - - +
1114 GLU* 3.1 11.4 - - + +
1124 LYS* 1.3 73.0 - - - +
1144 TYR* 1.3 60.6 + - - +
1154 SER* 3.7 10.7 + - - -
1164 THR* 2.7 35.0 + - - +
1174 ARG* 3.2 20.0 + - - +
1028 TYR* 5.4 1.0 + - - -
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Residues in contact with TYR 114 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1124 LYS* 3.2 41.6 + - + +
1134 ASP* 1.3 72.1 + - - +
1154 SER* 1.3 60.0 + - - +
1174 ARG* 3.5 7.4 + - + +
1184 ALA* 3.0 31.0 + - - +
1028 TYR* 3.6 50.2 - + + -
1058 ALA* 3.7 20.9 - - + -
1068 ALA* 3.5 20.0 - - + +
1098 GLU* 2.8 38.1 + - - -
1178 ARG* 3.4 20.5 + - - -
1248 ILE* 3.5 11.9 - - + +
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Residues in contact with SER 115 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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604 TYR* 3.1 17.8 + - - -
644 ARG* 3.3 25.2 + - - -
1134 ASP* 3.3 5.5 + - - -
1144 TYR* 1.3 79.0 - - - +
1164 THR* 1.3 56.6 + - - +
1184 ALA* 3.5 2.9 + - - +
1194 PHE* 3.1 23.9 + - - +
1028 TYR* 2.6 30.6 + - - -
1248 ILE* 3.9 10.6 + - - +
1258 ASN* 4.9 1.0 - - - +
1288 VAL* 3.8 16.5 - - - +
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Residues in contact with THR 116 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24 LEU* 3.6 9.5 - - - +
64 MET* 3.8 23.8 - - + -
104 LEU* 4.1 17.7 - - + -
604 TYR* 3.0 21.7 + - + -
1084 ALA* 4.3 3.8 - - + -
1134 ASP* 2.7 33.1 + - - -
1144 TYR 3.4 0.2 - - - -
1154 SER* 1.3 74.0 - - - +
1174 ARG* 1.3 60.5 + - - +
1194 PHE* 3.2 2.0 + - + +
1204 LEU* 3.0 45.4 + - + +
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Residues in contact with ARG 117 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1054 ALA* 3.8 26.0 - - - +
1084 ALA* 3.8 10.9 - - + +
1094 GLU* 3.2 29.1 + - + +
1134 ASP 3.2 14.9 + - - +
1144 TYR* 3.8 9.2 - - + +
1164 THR* 1.3 79.3 - - - +
1184 ALA* 1.3 61.5 + - - +
1204 LEU* 3.5 5.0 + - - +
1214 GLU* 3.0 36.2 + - - +
1244 ILE* 3.5 20.3 - - - +
1178 ARG* 5.2 11.2 - - - +
1218 GLU* 5.2 1.9 + - - +
1149 TYR* 3.5 28.0 + - - +
1179 ARG* 4.9 12.9 - - - +
1189 ALA* 5.8 0.2 - - - +
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Residues in contact with ALA 118 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1144 TYR 3.0 18.4 + - - +
1154 SER 3.8 4.0 - - - +
1164 THR 3.3 0.4 - - - -
1174 ARG* 1.3 73.8 - - - +
1194 PHE* 1.3 63.8 + - - +
1214 GLU* 3.4 16.0 - - - +
1224 TRP 4.6 0.9 + - - -
1178 ARG* 6.1 0.4 - - - +
1218 GLU* 3.7 29.1 - - - +
1248 ILE* 4.0 12.1 - - + -
1258 ASN* 3.4 31.5 + - - +
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Residues in contact with PHE 119 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104 LEU* 4.3 3.6 - - + -
564 ARG* 3.6 23.1 - - + -
574 PHE* 3.5 34.3 - + - -
604 TYR* 3.5 53.6 - + + -
1154 SER 3.1 15.5 + - - +
1164 THR* 3.2 11.0 + - + +
1184 ALA* 1.3 77.9 - - - +
1204 LEU* 1.3 68.5 + - + +
1214 GLU 3.2 1.1 + - - -
1224 TRP* 3.5 17.7 + - + +
1234 PHE* 3.4 30.5 - + - -
1258 ASN* 4.1 4.7 + - - +
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Residues in contact with LEU 120 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104 LEU* 5.0 0.9 - - + -
574 PHE* 4.1 24.5 - - + -
1014 ILE* 4.4 14.8 - - + +
1044 LEU* 3.7 58.3 - - + +
1054 ALA* 3.9 7.9 - - + +
1084 ALA* 4.7 0.7 - - + -
1164 THR* 3.0 34.3 + - + +
1174 ARG* 4.0 7.4 - - - +
1184 ALA 3.4 0.4 - - - -
1194 PHE* 1.3 77.9 - - + +
1214 GLU* 1.3 63.0 + - - +
1224 TRP 3.2 2.7 - - - -
1234 PHE* 3.1 9.6 + - + +
1244 ILE* 3.0 34.1 + - + +
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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