Contacts of the helix formed by residues 1003 - 1012 (chain E) in PDB entry 5B2G
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 ILE1003 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1002E ASN* 1.3 81.6 - - + +
1004E PHE* 1.3 66.7 + - + +
1005E GLU 3.5 0.5 + - - -
1006E MET* 3.5 16.9 + - + +
1007E LEU* 3.6 30.6 + - + +
1067E PHE* 4.9 4.7 - - + -
1068E ASN* 5.2 9.2 - - - +
1093E ALA* 5.1 11.0 - - + +
1094E VAL* 5.8 7.2 - - + -
1097E ALA* 4.2 25.6 - - + -
1158E TRP* 6.2 1.8 - - - +
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Residues in contact with PHE1004 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1002E ASN* 3.6 34.3 - - + -
1003E ILE* 1.3 83.2 - - + +
1005E GLU* 1.3 84.4 + - + +
1007E LEU* 3.3 7.9 + - - +
1008E ARG* 3.0 51.3 + - + +
1029E ILE* 5.5 7.0 - - + +
1064E GLU* 3.4 39.7 - - + +
1067E PHE* 5.1 8.7 - - + -
1068E ASN* 6.1 1.6 - - - +
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Residues in contact with GLU1005 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1002E ASN 3.2 32.5 + - - +
1004E PHE* 1.3 95.2 - - + +
1006E MET* 1.3 70.0 + - + +
1008E ARG* 3.3 10.7 + - - +
1009E ILE* 3.1 23.9 + - - +
1158E TRP* 6.0 2.1 - - - -
1161E TYR* 5.2 11.6 - - + +
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Residues in contact with MET1006 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1002E ASN 4.7 3.8 - - - +
1003E ILE* 3.5 10.9 + - + +
1004E PHE 3.3 0.6 - - - -
1005E GLU* 1.3 83.8 - - + +
1007E LEU* 1.3 82.1 + - + +
1009E ILE* 2.9 27.7 + - - +
1010E ASP* 3.5 8.3 + - - +
1094E VAL 5.9 1.1 - - - +
1097E ALA* 4.3 23.3 - - + +
1098E ALA* 4.7 7.2 - - - +
1101E ASN* 3.4 33.4 - - + +
1149E VAL* 5.9 1.6 - - - -
1152E THR* 5.3 7.9 - - - -
1161E TYR* 4.0 39.0 - - + +
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Residues in contact with LEU1007 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1003E ILE* 3.6 25.9 + - + +
1004E PHE 3.3 7.5 + - - +
1005E GLU 3.2 0.2 - - - -
1006E MET* 1.3 84.1 - - + +
1008E ARG* 1.3 64.3 + - - +
1009E ILE 3.3 0.2 - - - -
1010E ASP* 3.7 15.0 + - + +
1011E GLU* 4.3 4.2 + - - +
1012E GLY 4.9 0.7 - - - +
1029E ILE* 4.3 11.3 - - + +
1067E PHE* 3.1 48.2 - - + -
1071E VAL* 5.1 2.7 - - + -
1097E ALA* 5.7 3.1 - - + +
1100E ILE* 5.8 3.8 - - + -
1101E ASN* 3.5 41.7 - - + +
1104E PHE* 4.9 10.8 - - + -
1145E ARG* 5.2 0.2 - - - +
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Residues in contact with ARG1008 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1004E PHE* 3.0 35.1 + - + +
1005E GLU* 3.6 14.8 - - - +
1006E MET 3.3 0.2 - - - -
1007E LEU* 1.3 77.7 - - - +
1009E ILE* 1.3 54.0 + - + +
1010E ASP 3.2 0.9 - - - -
1012E GLY* 2.8 43.9 + - - +
1013E LEU* 3.3 54.2 - - + +
1015E LEU* 6.0 1.0 - - - +
1029E ILE* 4.5 19.2 - - + +
1060E LYS* 4.0 40.2 + - - +
1064E GLU* 6.3 1.0 - - - +
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Residues in contact with ILE1009 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1005E GLU 3.1 12.2 + - - +
1006E MET* 2.9 21.1 - - - +
1008E ARG* 1.3 75.4 - - - +
1010E ASP* 1.3 63.7 + - - +
1011E GLU 5.1 0.2 - - - -
1012E GLY* 4.3 3.7 + - - +
1148E ARG* 5.0 14.7 + - - +
1161E TYR* 3.3 38.4 - - + +
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Residues in contact with ASP1010 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1006E MET 3.5 10.8 + - - +
1007E LEU* 3.9 13.1 - - + +
1008E ARG 3.2 1.2 - - - -
1009E ILE* 1.3 83.0 - - - +
1011E GLU* 1.3 64.0 + - + +
1101E ASN* 2.6 38.5 + - - +
1145E ARG* 3.0 56.1 + - - +
1148E ARG* 5.9 0.2 + - - -
1149E VAL* 4.4 0.7 - - - +
1161E TYR* 3.9 15.8 + - - -
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Residues in contact with GLU1011 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1007E LEU 4.3 3.6 + - - +
1008E ARG 3.9 0.6 + - - -
1009E ILE 5.1 0.2 - - - -
1010E ASP* 1.3 81.4 - - + +
1012E GLY* 1.3 61.6 + - - +
1018E TYR* 3.6 39.8 + - + +
1030E GLY* 5.0 14.8 - - - +
1104E PHE* 5.1 11.8 - - - +
1105E GLN* 5.2 10.0 - - - +
1145E ARG* 4.2 16.7 + - - +
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Residues in contact with GLY1012 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1007E LEU 4.9 1.0 - - - +
1008E ARG* 2.8 26.9 + - - +
1009E ILE* 4.3 2.9 - - - -
1010E ASP 3.6 1.2 - - - +
1011E GLU* 1.3 83.0 - - - +
1013E LEU* 1.3 59.8 + - - +
1014E ARG* 4.2 1.1 - - - -
1018E TYR* 6.6 0.2 - - - -
1029E ILE* 5.1 7.6 - - - +
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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