Contacts of the helix formed by residues 1093 - 1103 (chain C) in PDB entry 2E9X
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 GLN1093 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1087C GLU* 5.2 6.3 + - - +
1088C LEU* 2.8 42.6 + - + +
1089C PRO 3.8 4.7 - - - +
1090C LYS* 3.0 40.5 + - + +
1092C TYR* 1.3 80.2 - - - +
1094C GLU* 1.3 66.6 + - - +
1095C GLY 3.2 4.5 + - - +
1096C TRP* 3.3 3.5 + - - -
1097C ARG* 3.1 26.7 + - - +
1130C GLU* 4.6 5.2 - - - +
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Residues in contact with GLU1094 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1093C GLN* 1.3 74.8 - - - +
1095C GLY* 1.3 65.7 + - - +
1097C ARG* 3.4 31.2 - - + +
1098C THR* 2.8 38.0 + - - +
1130C GLU* 4.4 1.4 + - - +
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Residues in contact with GLY1095 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1090C LYS* 5.9 7.0 - - - -
1093C GLN* 3.2 4.6 + - - +
1094C GLU* 1.3 82.5 - - - +
1096C TRP* 1.3 61.1 + - - +
1098C THR* 3.2 5.6 + - - -
1099C VAL* 3.1 24.4 + - - +
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Residues in contact with TRP1096 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1090C LYS* 3.3 44.6 + - + +
1091C ILE* 3.4 32.3 - - - +
1093C GLN 3.3 3.0 + - - +
1095C GLY* 1.3 74.5 - - - +
1097C ARG* 1.3 57.7 + - - +
1099C VAL* 3.2 29.5 + - + +
1100C PHE* 2.8 49.4 + + + -
1107C VAL* 4.7 4.9 - - + -
1112C MET* 3.5 33.0 - - + +
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Residues in contact with ARG1097 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1091C ILE 4.7 1.7 + - - +
1092C TYR* 2.7 35.7 + - - +
1093C GLN 3.1 18.4 + - - +
1094C GLU* 3.4 31.8 - - + +
1096C TRP* 1.3 77.0 - - - +
1098C THR* 1.3 57.4 + - - +
1100C PHE* 3.7 6.9 - - - +
1101C SER* 3.0 25.5 + - - -
1130C GLU* 2.7 34.1 + - - +
1133C ASP* 3.8 48.4 + - - +
1134C ILE* 4.1 10.6 - - - +
1137C SER* 3.2 27.4 + - - +
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Residues in contact with THR1098 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1094C GLU* 2.8 32.1 + - - +
1095C GLY* 3.5 5.1 - - - -
1097C ARG* 1.3 75.7 - - - +
1099C VAL* 1.3 67.2 + - + +
1101C SER* 3.1 22.4 - - - -
1102C ALA* 3.2 8.0 + - - +
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Residues in contact with VAL1099 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1095C GLY 3.1 14.0 + - - +
1096C TRP* 3.6 34.8 - - + +
1098C THR* 1.3 75.4 - - + +
1100C PHE* 1.3 67.0 + - + +
1102C ALA* 3.2 20.5 + - + +
1103C ASP 3.7 5.7 + - - +
1106C VAL* 5.0 7.2 - - + +
1107C VAL* 4.8 6.3 - - + -
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Residues in contact with PHE1100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1091C ILE* 4.6 3.1 - - + -
1096C TRP* 2.8 50.8 + + + +
1097C ARG* 3.7 9.6 - - - +
1099C VAL* 1.3 76.2 - - - +
1101C SER* 1.3 61.4 + - - +
1103C ASP 3.2 1.1 + - - -
1104C PRO* 3.0 36.6 - - + +
1107C VAL* 3.3 45.5 - - + -
1109C LEU* 3.6 17.7 - - + -
1112C MET* 4.1 9.9 - - + -
1116C PHE* 3.5 33.4 - + - -
1137C SER* 5.0 3.8 - - - +
1141C THR* 3.2 34.3 - - + +
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Residues in contact with SER1101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1097C ARG 3.0 15.1 + - - -
1098C THR* 3.1 18.8 + - - -
1100C PHE* 1.3 77.5 - - - +
1102C ALA* 1.3 58.8 + - - +
1103C ASP* 3.3 0.6 + - - -
1104C PRO* 4.6 6.2 - - - +
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Residues in contact with ALA1102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1098C THR 3.2 9.1 + - - +
1099C VAL* 3.2 14.0 + - + +
1100C PHE 3.2 1.0 - - - -
1101C SER* 1.3 78.5 - - - +
1103C ASP* 1.3 65.2 + - + +
1104C PRO* 4.4 0.2 - - - -
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Residues in contact with ASP1103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1099C VAL 3.7 3.0 + - - +
1100C PHE 3.2 5.0 + - - +
1102C ALA* 1.3 85.5 - - + +
1104C PRO* 1.3 68.0 - - - +
1105C ASN* 3.6 18.6 + - - +
1106C VAL* 2.9 51.6 + - + +
1107C VAL* 4.2 1.4 + - - +
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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