Contacts of the helix formed by residues 1168 - 1177 (chain I) in PDB entry 2X4Y
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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1197G GLN* 4.1 17.9 + - - +
1200G SER* 4.5 15.9 + - - -
1201G LYS* 6.1 3.2 - - - +
1164I PRO 5.6 0.2 + - - -
1166I GLY 5.3 0.2 - - - -
1167I VAL* 1.3 88.0 - - + +
1169I GLN* 1.3 58.1 + - - +
1170I ASP* 3.0 21.8 + - - +
1171I LEU* 3.1 30.0 + - + +
1172I ASP* 3.0 31.9 + - - +
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Residues in contact with GLN1169 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1167I VAL 4.2 0.6 - - - -
1168I ASN* 1.3 72.9 + - - +
1170I ASP* 1.3 64.8 + - - +
1172I ASP* 3.3 9.7 + - - +
1173I LYS* 2.8 56.5 + - + +
1192I TYR* 5.3 6.7 + - - +
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Residues in contact with ASP1170 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1193G HIS* 3.2 45.2 + - - +
1196G LEU* 3.3 39.2 - - + +
1197G GLN* 3.5 14.6 + - + +
1199G ARG* 5.8 0.3 + - - -
1200G SER* 5.8 1.7 - - - -
1168I ASN* 3.0 8.6 + - - +
1169I GLN* 1.3 82.3 - - - +
1171I LEU* 1.3 65.5 + - - +
1173I LYS* 3.4 3.3 + - - +
1174I GLU* 2.9 18.9 + - - +
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Residues in contact with LEU1171 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1197G GLN* 3.5 27.2 - - - +
1090I TRP* 3.8 27.8 - - + -
1163I VAL* 3.8 27.6 - - + -
1164I PRO 4.1 5.4 - - - +
1167I VAL* 6.2 0.9 - - + -
1168I ASN* 3.1 32.5 + - + +
1170I ASP* 1.3 76.9 - - - +
1172I ASP* 1.3 63.5 + - - +
1174I GLU* 3.2 4.9 + - - +
1175I LYS* 2.9 44.2 + - + +
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Residues in contact with ASP1172 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1090I TRP* 2.9 25.1 + - - +
1164I PRO 4.5 0.5 - - - +
1165I LEU* 3.9 0.5 - - - -
1166I GLY* 3.0 33.3 + - - -
1167I VAL 4.6 0.3 + - - -
1168I ASN 3.0 18.7 + - - +
1169I GLN* 3.5 11.1 - - - +
1171I LEU* 1.3 82.5 - - - +
1173I LYS* 1.3 56.8 + - + +
1175I LYS* 3.2 2.8 + - - +
1176I MET* 3.0 35.4 + - + +
1192I TYR* 2.7 40.8 + - + +
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Residues in contact with LYS1173 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1193G HIS* 3.6 41.6 - - + +
1169I GLN* 2.8 49.2 + - + +
1170I ASP* 3.9 4.0 + - - +
1171I LEU 3.3 0.2 - - - -
1172I ASP* 1.3 71.7 - - + +
1174I GLU* 1.3 65.5 + - - +
1176I MET* 3.4 23.6 + - + +
1177I LEU* 3.4 21.4 + - + +
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Residues in contact with GLU1174 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1190G ILE* 4.0 20.9 - - + +
1193G HIS* 4.1 11.3 - - + +
1194G ARG* 3.2 36.3 + - + +
1197G GLN* 2.6 34.6 + - - +
1170I ASP 2.9 17.3 + - - +
1171I LEU* 3.5 5.9 - - - +
1173I LYS* 1.3 74.1 - - - +
1175I LYS* 1.3 75.4 + - + +
1177I LEU* 3.1 19.7 + - - +
1178I GLU* 3.6 8.3 + - - +
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Residues in contact with LYS1175 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1090I TRP* 3.6 47.4 - - + -
1097I PRO* 5.6 0.2 - - - +
1098I SER* 3.7 21.4 + - - +
1163I VAL* 4.2 27.9 - - - +
1171I LEU* 2.9 31.3 + - + +
1172I ASP 3.2 0.2 + - - -
1174I GLU* 1.3 88.4 + - + +
1176I MET* 1.3 62.6 + - - +
1178I GLU* 3.1 42.1 + - - +
1179I GLY 4.8 0.2 + - - -
1188I VAL* 4.7 3.1 - - - +
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Residues in contact with MET1176 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1090I TRP* 3.6 17.5 - - + -
1172I ASP* 3.0 28.1 + - + +
1173I LYS* 3.8 20.9 - - + +
1174I GLU 3.3 0.4 - - - -
1175I LYS* 1.3 75.8 - - - +
1177I LEU* 1.3 63.6 + - + +
1178I GLU 3.6 0.5 + - - -
1179I GLY 4.6 0.7 + - - -
1185I ARG* 3.8 23.9 - - - +
1188I VAL* 4.2 17.8 - - + +
1189I GLN* 4.1 26.0 + - + +
1192I TYR* 3.7 44.2 - - + -
1193I HIS* 5.1 4.5 - - - +
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Residues in contact with LEU1177 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1186G LYS* 2.9 45.3 + - + +
1189G GLN* 3.7 42.0 - - + +
1190G ILE* 3.8 26.2 - - + +
1193G HIS* 4.2 11.4 - - + +
1173I LYS* 3.4 17.3 - - + +
1174I GLU 3.1 7.9 + - - +
1175I LYS 3.0 1.4 - - - -
1176I MET* 1.3 81.9 - - + +
1178I GLU* 1.3 56.7 + - - +
1179I GLY 3.3 2.9 - - - +
1185I ARG* 4.0 10.3 - - - +
1189I GLN* 6.2 2.0 - - - +
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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