Contacts of the helix formed by residues 118 - 127 (chain E) in PDB entry 1GEC
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 GLU 118 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117E ASN* 1.3 71.7 - - - +
119E GLY* 1.3 66.1 + - - +
121E LEU* 3.1 5.4 + - - +
122E LEU* 3.1 40.0 + - + +
195E ARG* 2.9 41.0 + - - +
196E ALA* 3.9 15.4 - - + +
200E SER* 5.7 0.6 - - - -
207E TYR* 3.5 34.4 - - + +
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Residues in contact with GLY 119 (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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117E ASN* 3.3 8.3 + - - +
118E GLU* 1.3 85.2 + - - +
120E SER* 1.3 60.2 + - - +
122E LEU* 3.4 6.8 + - - +
123E ASN* 3.1 22.7 + - - +
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Residues in contact with SER 120 (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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113E VAL* 3.7 17.9 - - - +
114E GLN* 3.3 33.8 + - - +
117E ASN* 2.9 20.1 + - - -
119E GLY* 1.3 68.7 - - - +
121E LEU* 1.3 65.7 + - - +
123E ASN* 3.3 9.3 + - - +
124E ALA* 3.0 23.0 + - - +
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Residues in contact with LEU 121 (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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113E VAL* 3.7 11.8 - - + +
117E ASN 3.4 10.0 + - - +
118E GLU* 3.1 11.1 + - - +
120E SER* 1.3 78.4 - - - +
122E LEU* 1.3 58.1 + - + +
124E ALA* 3.3 1.8 + - - +
125E ILE* 2.9 50.7 + - + +
130E VAL* 4.3 10.5 - - + -
132E VAL* 4.2 13.2 - - + -
175E ILE* 4.6 14.4 - - + -
206E VAL* 4.2 13.2 - - + +
207E TYR* 3.8 30.3 - - + -
210E SER* 3.5 28.7 - - - +
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Residues in contact with LEU 122 (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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1E LEU 5.1 2.7 - - - +
118E GLU* 3.1 41.9 + - + +
119E GLY* 3.8 7.4 - - - +
121E LEU* 1.3 78.9 - - + +
123E ASN* 1.3 59.2 + - - +
125E ILE* 4.3 3.6 - - + +
126E ALA* 2.8 32.7 + - - +
166E TYR* 3.7 37.1 - - + -
168E LYS* 6.1 0.4 - - - +
175E ILE* 3.6 30.1 - - + -
195E ARG* 3.8 18.6 - - - +
207E TYR* 5.9 0.2 - - - +
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Residues in contact with ASN 123 (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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1E LEU* 4.0 24.6 + - - +
119E GLY 3.1 15.5 + - - +
120E SER* 3.3 11.9 + - - +
122E LEU* 1.3 76.0 - - - +
124E ALA* 1.3 55.3 + - - +
126E ALA* 3.6 5.4 - - - +
127E HIS* 2.6 49.2 + - - -
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Residues in contact with ALA 124 (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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113E VAL* 3.9 21.3 - - + -
120E SER 3.0 13.2 + - - +
121E LEU 3.7 7.0 - - - +
122E LEU 3.2 0.2 - - - -
123E ASN* 1.3 76.1 - - - +
125E ILE* 1.3 64.9 + - - +
126E ALA 3.2 0.4 - - - -
127E HIS* 3.1 14.5 + - - +
128E GLN* 2.9 21.3 + - - +
130E VAL* 3.7 18.3 - - + +
212E TYR* 4.6 11.4 - - + -
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Residues in contact with ILE 125 (chain E).
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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5E VAL* 3.7 22.9 - - + -
7E TRP* 2.9 30.4 + - - +
121E LEU* 2.9 35.6 + - + +
122E LEU* 3.8 15.7 - - + +
124E ALA* 1.3 75.4 - - - +
126E ALA* 1.3 58.6 - - - +
127E HIS 2.9 6.8 + - - -
128E GLN 2.9 9.2 + - - -
130E VAL* 4.1 13.5 - - + -
163E ALA* 3.8 29.8 - - + +
165E GLY 3.8 21.8 - - - +
166E TYR* 3.9 5.6 - - + -
175E ILE* 4.3 14.1 - - + -
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Residues in contact with ALA 126 (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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1E LEU* 3.4 45.1 - - + +
2E PRO* 4.5 3.3 - - + +
5E VAL* 4.2 15.5 - - - +
7E TRP* 3.6 12.0 - - - -
122E LEU 2.8 18.0 + - - +
123E ASN 3.6 8.1 - - - +
124E ALA 3.2 0.2 - - - -
125E ILE* 1.3 77.0 - - - +
127E HIS* 1.3 59.5 + - - +
166E TYR* 4.1 6.5 - - - +
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Residues in contact with HIS 127 (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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1E LEU* 4.2 19.1 - - + +
7E TRP* 3.4 9.7 - - - -
37E ILE* 4.6 2.9 - - - +
40E ILE* 3.6 13.7 - - - +
123E ASN* 2.6 49.1 + - - -
124E ALA* 3.1 7.9 + - - +
125E ILE 3.0 0.8 - - - -
126E ALA* 1.3 82.0 - - + +
128E GLN* 1.3 78.1 + - - +
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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