Contacts of the helix formed by residues 183 - 188 (chain G) in PDB entry 1GLE
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 TYR 183 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182G ASP* 1.3 77.0 + - - +
184G THR* 1.4 68.1 + - - +
186G ALA* 3.2 13.6 + - - +
187G SER* 3.3 12.5 + - - -
192G PHE* 4.5 10.6 - + - -
197G LEU* 3.9 39.6 + - + +
217G VAL* 4.1 26.5 + - + -
218G ARG* 3.2 11.7 + - - +
219G ARG* 2.9 52.7 - - + -
220G SER* 4.2 7.9 - - - +
290G ILE* 4.6 17.0 - - + +
298G VAL* 4.1 22.2 - - + -
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Residues in contact with THR 184 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182G ASP* 2.7 35.4 + - - +
183G TYR* 1.4 69.3 - - - +
185G ASN* 1.3 59.7 + - - +
187G SER* 2.3 29.9 + - - -
188G ARG* 3.4 8.9 - - - +
220G SER* 4.3 7.2 - - - +
243G ALA* 3.1 4.2 - - - -
244G GLY* 2.8 17.7 + - - -
247G GLN* 3.6 27.8 + - + -
290G ILE* 3.1 33.7 - - + +
291G ALA* 4.0 8.1 - - - -
292G CYS* 4.5 4.5 - - - -
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Residues in contact with ASN 185 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81G ASN* 3.0 35.1 + - - +
83G ARG* 4.1 14.8 - - - +
84G GLU 5.6 0.6 - - - +
164G THR* 3.9 12.9 + - - +
166G ASP* 3.2 23.0 + - - +
181G THR* 3.2 22.4 - - - +
182G ASP* 2.6 25.6 + - - +
184G THR* 1.3 71.3 - - - +
186G ALA* 1.3 64.9 + - - +
188G ARG* 3.1 23.2 + - - +
189G THR* 4.1 2.3 + - - -
242G ILE* 4.0 0.7 - - - +
243G ALA 3.9 1.0 - - - -
244G GLY* 3.5 13.2 + - - -
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Residues in contact with ALA 186 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164G THR* 6.4 0.2 - - - -
181G THR* 3.7 15.2 - - + +
182G ASP 3.2 15.5 + - - +
183G TYR 3.2 4.0 + - - +
185G ASN* 1.3 80.2 - - - +
187G SER* 1.3 64.5 + - - +
188G ARG 2.9 1.1 + - - -
189G THR* 3.1 28.8 - - - +
192G PHE* 3.4 33.8 - - + +
199G TRP* 4.6 8.3 - - + -
217G VAL* 4.7 2.7 - - + -
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Residues in contact with SER 187 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128G THR* 4.4 6.7 - - - +
130G LEU* 3.6 20.2 - - - +
183G TYR 3.3 6.8 + - - -
184G THR* 2.3 35.7 + - - -
186G ALA* 1.3 77.3 - - - +
188G ARG* 1.3 59.7 + - - +
189G THR 3.4 0.9 + - - -
190G MET* 4.0 3.5 + - - -
192G PHE* 4.5 15.9 - - - +
194G ILE* 4.1 20.0 - - - -
289G THR* 3.6 24.4 + - - -
290G ILE* 4.2 9.4 + - - +
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Residues in contact with ARG 188 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83G ARG* 3.0 29.8 - - + +
84G GLU* 2.7 43.5 + - + +
130G LEU* 3.7 6.0 - - - +
135G TYR* 3.2 17.4 + - - -
136G PHE* 2.8 47.5 - - - +
137G SER* 4.4 1.8 - - - +
164G THR* 6.4 1.1 - - + -
184G THR 3.4 10.5 - - - +
185G ASN* 3.1 19.1 - - - +
186G ALA 2.9 0.6 - - - -
187G SER* 1.3 86.1 - - - +
189G THR* 1.3 51.4 + - - +
190G MET 3.4 0.9 - - - -
247G GLN* 4.4 3.6 - - - +
287G LEU* 3.5 22.5 - - - +
289G THR* 3.6 25.9 + - - +
303G GLU* 2.9 35.2 + - - -
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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