Contacts of the helix formed by residues 1168 - 1177 (chain E) in PDB entry 2X4X
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 ASN1168 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1197A GLN* 4.2 16.0 + - - +
1200A SER* 4.9 14.4 + - - -
1201A LYS* 6.1 2.4 - - - +
1205A GLU 5.0 6.3 + - - -
1164E PRO 5.5 2.2 + - - +
1166E GLY 5.3 0.2 - - - -
1167E VAL* 1.3 79.0 - - + +
1169E GLN* 1.3 59.2 + - - +
1170E ASP* 3.0 21.8 + - - +
1171E LEU* 3.1 29.0 + - + +
1172E ASP* 2.9 33.8 + - - +
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Residues in contact with GLN1169 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1167E VAL 4.1 2.0 + - - -
1168E ASN* 1.3 73.3 + - - +
1170E ASP* 1.3 62.2 + - - +
1172E ASP* 3.4 8.9 + - - +
1173E LYS* 3.0 61.9 + - + +
1192E TYR* 5.4 4.3 + - - -
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Residues in contact with ASP1170 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1193A HIS* 3.4 38.5 + - - +
1196A LEU* 3.5 39.7 - - + +
1197A GLN* 3.5 22.4 + - + -
1199A ARG* 5.8 0.2 + - - -
1200A SER* 4.8 5.4 + - - -
1168E ASN* 3.0 5.9 + - - +
1169E GLN* 1.3 80.5 - - - +
1171E LEU* 1.3 60.3 + - - +
1173E LYS* 3.4 4.6 + - - +
1174E GLU 3.0 23.2 + - - -
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Residues in contact with LEU1171 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1197A GLN* 3.6 26.3 - - - +
1090E TRP* 5.3 0.2 - - + -
1163E VAL* 4.1 20.2 - - + -
1164E PRO* 4.7 8.1 - - + +
1168E ASN* 3.1 30.7 + - + +
1170E ASP* 1.3 73.2 - - - +
1172E ASP* 1.3 71.1 + - - +
1174E GLU* 3.2 9.3 + - - +
1175E LYS* 2.9 56.9 + - + +
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Residues in contact with ASP1172 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1090E TRP* 2.9 26.4 + - - +
1164E PRO 4.4 2.4 - - - +
1165E LEU* 3.9 1.0 - - - -
1166E GLY* 3.0 33.4 + - - -
1167E VAL 4.7 0.3 + - - -
1168E ASN 2.9 19.2 + - - +
1169E GLN* 3.6 10.2 - - - +
1170E ASP 3.3 0.2 - - - -
1171E LEU* 1.3 78.0 - - - +
1173E LYS* 1.3 63.7 + - + +
1175E LYS* 3.3 2.8 + - - +
1176E MET* 3.0 29.3 + - + +
1192E TYR* 2.9 41.5 + - + +
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Residues in contact with LYS1173 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1193A HIS* 3.6 41.5 - - + +
1169E GLN* 3.0 54.6 + - + +
1170E ASP* 3.8 3.4 + - - +
1171E LEU 3.2 0.2 - - - -
1172E ASP* 1.3 77.1 - - + +
1174E GLU* 1.3 62.0 + - - +
1176E MET* 3.4 25.7 + - + +
1177E LEU* 3.5 19.6 - - - +
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Residues in contact with GLU1174 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1190A ILE* 4.2 18.3 - - + +
1193A HIS* 4.1 13.3 - - + +
1194A ARG* 3.1 38.2 + - + +
1197A GLN* 2.7 32.2 + - - +
1170E ASP 3.0 17.5 + - - +
1171E LEU* 3.6 11.7 - - - +
1173E LYS* 1.3 74.1 - - - +
1175E LYS* 1.3 69.9 + - + +
1177E LEU* 3.1 21.6 + - - +
1178E GLU* 3.7 4.9 + - - +
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Residues in contact with LYS1175 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1090E TRP* 3.5 46.5 - - + +
1098E SER* 3.9 29.2 + - - +
1163E VAL* 3.9 27.8 - - - +
1171E LEU* 2.9 43.5 + - + +
1172E ASP 3.6 1.1 - - - +
1174E GLU* 1.3 78.9 - - + +
1176E MET* 1.3 63.6 + - - +
1177E LEU 3.0 1.4 + - - -
1178E GLU* 3.1 30.2 + - - +
1188E VAL* 4.7 2.8 - - - +
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Residues in contact with MET1176 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1090E TRP* 3.6 20.2 - - + -
1172E ASP* 3.0 19.8 + - + +
1173E LYS* 3.8 25.1 - - + +
1174E GLU 3.1 0.8 - - - -
1175E LYS* 1.3 78.1 - - - +
1177E LEU* 1.3 63.3 + - + +
1178E GLU 3.4 0.6 + - - -
1179E GLY 4.8 0.5 + - - -
1185E ARG* 3.8 21.3 - - - +
1188E VAL* 4.2 20.3 - - + +
1189E GLN* 4.3 25.2 + - + +
1192E TYR* 3.7 42.8 - - + -
1193E HIS* 5.3 4.0 - - + -
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Residues in contact with LEU1177 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1186A LYS* 2.7 51.6 + - + +
1189A GLN* 3.7 39.3 - - + +
1190A ILE* 3.6 36.1 - - + +
1193A HIS* 4.4 6.7 - - + +
1173E LYS 3.5 16.4 - - - +
1174E GLU 3.1 4.2 + - - +
1175E LYS 3.0 1.2 - - - -
1176E MET* 1.3 84.2 - - + +
1178E GLU* 1.3 56.8 + - - +
1179E GLY 3.4 3.7 + - - +
1185E ARG* 4.3 8.5 - - - +
1189E GLN* 6.1 2.7 - - - +
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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