Contacts of the helix formed by residues 1084 - 1098 (chain X) in PDB entry 2OO8
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 SER1084 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1017X THR* 6.0 3.6 - - - -
1018X ASN* 6.1 0.7 - - - +
1021X VAL* 4.8 2.0 - - - -
1082X ARG 3.9 0.2 + - - -
1083X PRO* 1.3 77.1 - - - +
1085X PHE* 1.3 58.8 + - - +
1086X ALA* 3.6 9.3 + - - +
1087X GLN* 2.9 37.2 + - - +
1088X ILE* 2.9 28.9 + - - +
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Residues in contact with PHE1085 (chain X).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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949X ALA* 3.8 16.2 - - - +
952X MET* 3.5 50.0 - - + -
953X ASP* 3.6 24.5 - - - +
956X SER* 4.0 3.6 - - - +
965X LEU* 3.9 4.9 - - + -
1017X THR* 3.9 25.7 - - + +
1020X ASP* 3.7 26.0 - - + -
1021X VAL* 3.6 21.7 - - + +
1024X TYR* 3.6 27.1 - + + -
1084X SER* 1.3 73.6 - - - +
1086X ALA* 1.3 56.9 + - - +
1088X ILE* 3.6 13.5 - - + +
1089X LEU* 2.9 30.0 + - - +
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Residues in contact with ALA1086 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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953X ASP* 3.5 26.2 + - - +
1084X SER* 3.2 8.8 + - - +
1085X PHE* 1.3 75.2 - - - +
1087X GLN* 1.3 66.2 + - + +
1089X LEU* 3.4 9.1 + - + +
1090X VAL* 3.1 33.0 + - + +
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Residues in contact with GLN1087 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1070X LEU* 5.6 0.2 - - - -
1082X ARG 4.8 0.3 - - - +
1083X PRO* 3.3 16.8 - - + +
1084X SER* 2.9 39.2 + - - +
1086X ALA* 1.3 74.4 - - + +
1088X ILE* 1.3 63.6 + - - +
1090X VAL* 3.5 6.4 + - - +
1091X SER* 2.9 29.1 + - - +
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Residues in contact with ILE1088 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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949X ALA* 3.9 5.4 - - + -
1021X VAL* 3.9 17.0 - - + -
1024X TYR* 3.6 35.0 - - + +
1070X LEU* 4.1 21.7 - - + +
1074X CYS* 3.9 22.4 - - - -
1083X PRO* 3.8 15.3 - - + -
1084X SER 2.9 18.2 + - - +
1085X PHE* 3.6 20.2 - - + +
1087X GLN* 1.3 75.8 - - - +
1089X LEU* 1.3 59.0 + - - +
1091X SER* 3.3 3.6 + - - -
1092X LEU* 2.9 42.5 + - + +
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Residues in contact with LEU1089 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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946X ALA* 3.4 31.9 - - + +
949X ALA* 4.0 9.0 - - + +
950X ARG* 3.9 38.8 - - + +
953X ASP* 5.1 9.9 - - + +
1085X PHE 2.9 17.9 + - - +
1086X ALA* 3.6 8.7 - - - +
1087X GLN 3.3 0.2 - - - -
1088X ILE* 1.3 76.9 - - - +
1090X VAL* 1.3 54.0 - - + +
1092X LEU* 3.3 3.8 + - - +
1093X ASN* 2.8 62.0 + - - +
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Residues in contact with VAL1090 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1086X ALA* 3.1 19.5 + - + +
1087X GLN* 4.0 6.5 - - - +
1089X LEU* 1.3 78.7 - - + +
1091X SER* 1.3 58.5 + - - +
1093X ASN* 3.3 10.9 + - - +
1094X ARG* 2.8 31.5 + - + +
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Residues in contact with SER1091 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1070X LEU* 4.3 20.8 - - - +
1087X GLN 2.9 17.2 + - - -
1088X ILE* 3.7 6.3 - - - -
1089X LEU 3.3 0.2 - - - -
1090X VAL* 1.3 78.4 - - - +
1092X LEU* 1.3 57.6 + - - +
1094X ARG* 3.3 30.3 + - - +
1095X MET* 3.0 36.9 + - - +
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Residues in contact with LEU1092 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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942X LEU* 4.1 29.3 - - + +
945X ALA* 3.6 25.8 - - + +
946X ALA* 3.8 14.8 - - + +
949X ALA* 4.3 1.8 - - + -
1024X TYR* 3.1 27.1 - - - +
1028X LEU* 4.7 6.1 - - + -
1067X VAL* 5.9 0.9 - - + -
1070X LEU* 3.9 20.0 - - + -
1088X ILE* 2.9 30.6 + - + +
1089X LEU* 3.7 4.0 - - - +
1091X SER* 1.3 76.5 - - - +
1093X ASN* 1.3 55.7 + - - +
1095X MET* 3.2 11.7 + - - +
1096X LEU* 2.9 34.8 + - - +
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Residues in contact with ASN1093 (chain X).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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943X HIS* 6.0 0.3 - - - -
946X ALA* 4.2 9.2 - - - +
950X ARG* 4.4 6.8 + - - +
1089X LEU* 2.8 50.1 + - - +
1090X VAL* 3.5 11.4 - - - +
1092X LEU* 1.3 67.9 - - - +
1094X ARG* 1.3 66.7 + - - +
1096X LEU* 3.4 9.2 + - - +
1097X GLU* 3.1 27.5 + - + +
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Residues in contact with ARG1094 (chain X).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1066X GLU* 2.6 34.1 + - - +
1090X VAL* 2.8 20.1 + - + +
1091X SER* 3.4 35.2 + - - +
1093X ASN* 1.3 72.2 - - - +
1095X MET* 1.3 81.3 + - - +
1097X GLU* 3.1 17.2 + - - +
1098X GLU* 3.4 27.3 + - + +
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Residues in contact with MET1095 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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939X GLN* 5.2 0.5 - - - +
942X LEU* 4.1 6.5 - - + -
1066X GLU* 3.3 53.4 - - + +
1067X VAL* 3.8 21.3 - - + +
1070X LEU* 4.9 9.2 - - + -
1091X SER* 3.0 19.4 + - - +
1092X LEU* 3.2 23.1 + - - +
1094X ARG* 1.3 89.9 - - - +
1096X LEU* 1.3 63.3 + - - +
1098X GLU* 3.1 14.3 + - - +
1100X LYS 4.6 0.3 - - - +
1102X TYR* 3.2 49.4 - - + +
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Residues in contact with LEU1096 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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939X GLN* 2.7 68.3 + - - +
942X LEU* 3.7 36.8 - - + +
943X HIS* 3.4 30.1 - - + +
946X ALA* 4.0 16.4 - - + -
1092X LEU 2.9 22.6 + - - +
1093X ASN* 3.8 10.3 - - - +
1094X ARG 3.3 0.2 - - - -
1095X MET* 1.3 76.0 - - - +
1097X GLU* 1.3 63.3 + - + +
1098X GLU 3.8 3.6 - - - +
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Residues in contact with GLU1097 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1093X ASN* 3.1 14.1 + - + +
1094X ARG* 3.1 13.5 + - - +
1096X LEU* 1.3 78.3 - - + +
1098X GLU* 1.3 63.6 + - + +
1099X ARG 3.9 0.3 + - - -
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Residues in contact with GLU1098 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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939X GLN* 4.7 5.0 - - - +
1066X GLU* 5.4 1.8 - - - +
1094X ARG* 3.4 29.0 + - + +
1095X MET* 3.1 10.6 + - - +
1096X LEU 3.8 7.3 - - - +
1097X GLU* 1.3 82.2 - - + +
1099X ARG* 1.3 62.7 - - - +
1100X LYS* 3.9 23.7 - - + +
1102X TYR* 2.6 28.4 + - + +
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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