Contacts of the helix formed by residues 1090 - 1096 (chain C) in PDB entry 3EI4
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 ASP1090 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6C VAL* 3.1 9.6 - - + +
58C TYR* 6.0 0.3 - - - -
998C PHE* 3.6 21.9 - - + -
1055C GLN* 3.5 7.2 + - - +
1070C HIS* 3.3 21.2 + - - -
1073C TRP* 5.0 0.2 + - - -
1074C ARG* 3.2 31.4 + - - +
1089C ILE* 1.3 74.8 - - - +
1091C GLY* 1.3 61.2 + - - +
1092C ASP* 4.2 9.1 - - + +
1093C LEU* 2.9 37.1 + - - +
1094C ILE* 3.2 10.4 + - - +
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Residues in contact with GLY1091 (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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5C TYR* 3.1 33.5 - - - -
6C VAL 2.7 13.8 + - - -
7C VAL* 3.9 7.2 - - - -
1089C ILE 3.6 3.2 + - - -
1090C ASP* 1.3 71.8 - - - +
1092C ASP* 1.3 53.9 + - - +
1094C ILE* 2.9 2.4 + - - -
1095C GLU* 2.4 44.5 + - - +
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Residues in contact with ASP1092 (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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6C VAL 4.1 1.7 - - - +
7C VAL* 3.5 7.4 - - - +
8C THR* 2.4 51.6 + - - +
38C ARG* 5.4 7.6 + - - +
1074C ARG* 5.4 6.9 + - - +
1090C ASP* 3.0 13.4 - - + +
1091C GLY* 1.3 77.0 - - - +
1093C LEU* 1.3 56.5 + - - +
1095C GLU* 4.1 5.3 - - - +
1096C SER* 3.3 22.9 + - - -
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Residues in contact with LEU1093 (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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58C TYR* 4.2 11.2 - - + +
1055C GLN* 3.5 24.7 - - + +
1058C LEU* 3.8 28.7 - - + +
1059C ASN* 3.3 23.6 - - - +
1062C ILE* 3.8 16.4 - - + -
1070C HIS* 3.4 35.7 - - + +
1090C ASP* 2.9 19.9 + - - +
1092C ASP* 1.3 75.1 - - - +
1094C ILE* 1.3 68.1 + - + +
1095C GLU 3.3 0.2 - - - -
1096C SER* 2.8 19.7 + - - +
1097C PHE 3.7 4.0 + - - -
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Residues in contact with ILE1094 (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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5C TYR* 3.5 16.4 - - + +
1051C LEU* 3.6 27.1 - - + +
1054C MET* 5.0 1.3 - - + -
1055C GLN* 3.7 22.7 - - + -
1058C LEU* 4.5 12.1 - - + -
1089C ILE* 3.5 29.8 - - + -
1090C ASP 3.7 5.2 - - - +
1091C GLY* 2.9 10.7 + - - +
1093C LEU* 1.3 81.9 - - + +
1095C GLU* 1.3 58.9 + - + +
1097C PHE* 3.0 27.4 - - - +
1133C VAL* 3.4 26.6 - - + +
1136C LEU* 4.2 12.8 - - + -
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Residues in contact with GLU1095 (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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5C TYR* 4.4 6.7 + - - +
7C VAL* 3.3 19.4 - - - +
8C THR 5.5 0.5 - - - +
1091C GLY 2.4 33.9 + - - +
1092C ASP* 4.7 5.3 - - - +
1094C ILE* 1.3 65.4 - - + +
1096C SER* 1.3 57.2 + - - +
1097C PHE 2.8 11.4 + - - -
1098C LEU* 3.1 21.4 + - + +
1099C ASP* 4.0 4.4 - - - +
1133C VAL* 4.0 7.0 - - + -
1136C LEU* 3.9 4.7 - - + +
1137C THR* 3.6 30.6 - - + +
1140C HIS* 3.2 32.5 + - - -
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Residues in contact with SER1096 (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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58C TYR* 5.3 1.7 + - - -
1058C LEU* 4.7 1.3 - - - -
1062C ILE* 3.9 18.0 - - - +
1092C ASP 3.3 16.7 + - - -
1093C LEU* 2.8 23.8 + - - +
1095C GLU* 1.3 75.6 - - - +
1097C PHE* 1.3 59.9 + - - +
1098C LEU 3.3 0.9 - - - -
1099C ASP* 3.5 27.1 + - - +
1100C ILE* 4.0 12.8 - - - +
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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