Contacts of the helix formed by residues 1168 - 1177 (chain O) 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 O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1197I GLN* 3.9 15.6 - - - +
1200I SER* 5.0 12.0 + - - -
1164O PRO 5.7 0.8 + - - +
1167O VAL* 1.3 85.9 - - + +
1169O GLN* 1.3 63.7 + - - +
1170O ASP* 3.2 15.4 + - - +
1171O LEU* 3.1 39.5 + - + +
1172O ASP* 2.9 25.4 + - - +
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Residues in contact with GLN1169 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1166O GLY 6.4 1.1 - - - -
1167O VAL 4.3 1.8 + - - +
1168O ASN* 1.3 73.5 - - - +
1170O ASP* 1.3 62.7 + - - +
1172O ASP* 3.3 10.7 + - - +
1173O LYS* 2.9 50.3 + - - +
1192O TYR* 5.4 3.1 - - - +
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Residues in contact with ASP1170 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1193I HIS* 2.8 56.1 + - - +
1196I LEU* 3.5 37.5 - - + +
1197I GLN* 3.6 8.2 + - + +
1199I ARG* 5.7 0.7 + - - -
1200I SER* 5.1 3.7 + - - +
1168O ASN* 3.2 10.4 + - - +
1169O GLN* 1.3 80.3 + - - +
1171O LEU* 1.3 65.8 + - - +
1173O LYS* 3.4 3.2 + - - +
1174O GLU* 3.0 20.4 + - - +
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Residues in contact with LEU1171 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1197I GLN* 3.5 28.0 - - - +
1090O TRP* 3.9 13.2 - - + +
1163O VAL* 3.8 33.7 - - + -
1164O PRO 3.9 5.6 - - - +
1168O ASN* 3.1 30.5 - - + +
1170O ASP* 1.3 78.0 - - - +
1172O ASP* 1.3 75.6 + - - +
1174O GLU* 3.3 4.5 + - - +
1175O LYS* 3.0 38.2 + - + +
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Residues in contact with ASP1172 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1090O TRP* 2.9 25.2 + - - +
1164O PRO 4.4 0.3 - - - +
1165O LEU* 3.8 1.2 - - - -
1166O GLY* 3.0 36.2 + - - -
1167O VAL 4.5 0.2 + - - -
1168O ASN 2.9 19.8 + - - +
1169O GLN* 3.3 9.6 + - - +
1171O LEU* 1.3 80.1 - - - +
1173O LYS* 1.3 57.0 + - + +
1175O LYS* 3.1 4.2 + - - +
1176O MET* 2.8 33.7 + - + +
1192O TYR* 2.8 40.7 + - + +
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Residues in contact with LYS1173 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1193I HIS* 3.4 39.9 - - + +
1169O GLN* 2.9 36.6 + - - +
1170O ASP* 3.8 4.5 + - - +
1172O ASP* 1.3 73.9 - - + +
1174O GLU* 1.3 64.3 + - - +
1176O MET* 3.3 24.7 + - + +
1177O LEU* 3.3 21.1 + - + +
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Residues in contact with GLU1174 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1190I ILE* 4.1 17.5 - - + +
1193I HIS* 4.2 11.3 - - + +
1194I ARG* 3.1 41.1 + - - +
1197I GLN* 2.9 25.1 + - - +
1170O ASP 3.0 14.4 + - - +
1171O LEU* 3.5 8.0 - - - +
1173O LYS* 1.3 75.8 - - - +
1175O LYS* 1.3 78.8 + - - +
1177O LEU* 3.0 19.8 + - - +
1178O GLU* 3.6 8.0 + - - +
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Residues in contact with LYS1175 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1090O TRP* 3.5 40.2 - - + +
1097O PRO* 5.3 0.5 - - - +
1098O SER* 3.5 30.7 - - - +
1163O VAL* 3.4 28.2 - - - +
1171O LEU* 3.0 34.6 + - + +
1172O ASP 3.4 7.4 - - - +
1174O GLU* 1.3 90.1 + - + +
1176O MET* 1.3 62.1 + - - +
1177O LEU 3.1 1.2 + - - -
1178O GLU* 3.2 26.8 + - - +
1179O GLY 4.9 0.2 + - - -
1188O VAL* 4.7 2.8 - - - +
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Residues in contact with MET1176 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1090O TRP* 3.6 17.0 - - + -
1172O ASP* 2.8 29.7 + - + +
1173O LYS* 3.8 19.1 - - + +
1174O GLU 3.1 0.8 - - - -
1175O LYS* 1.3 77.9 - - - +
1177O LEU* 1.3 62.3 + - + +
1178O GLU 3.2 1.5 + - - -
1179O GLY 4.6 1.0 + - - -
1185O ARG* 4.0 20.3 - - - +
1188O VAL* 3.9 22.0 - - + +
1189O GLN* 3.9 27.5 + - + +
1192O TYR* 3.8 42.0 - - + +
1193O HIS* 5.4 3.6 - - - -
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Residues in contact with LEU1177 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1186I LYS* 2.8 44.9 + - + +
1189I GLN* 3.7 45.1 - - + +
1190I ILE* 3.7 27.1 - - + +
1193I HIS* 4.3 10.3 - - + +
1173O LYS* 3.4 15.9 - - + +
1174O GLU* 3.0 9.6 + - - +
1176O MET* 1.3 81.8 - - + +
1178O GLU* 1.3 59.3 + - - +
1179O GLY 3.5 1.6 + - - +
1185O ARG* 4.1 11.2 - - - +
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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