Contacts of the strand formed by residues 237 - 243 (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 ILE 237 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71G SER* 5.2 10.9 + - - +
74G ILE* 2.8 41.0 + - - +
77G ILE* 4.5 3.0 - - - +
226G GLN* 3.1 9.5 - - + -
227G THR* 2.6 58.0 + - - +
228G ASN* 5.5 0.2 - - - -
229G ILE* 5.8 4.3 - - - +
238G PRO* 1.3 73.8 + - + +
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Residues in contact with PRO 238 (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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74G ILE 4.9 0.7 - - - +
75G ALA 3.3 24.5 - - - +
76G ALA* 3.7 6.4 - - + +
77G ILE* 2.9 24.8 + - - +
223G VAL* 3.5 17.5 - - + -
225G GLY 2.8 8.5 - - - +
226G GLN* 3.3 18.2 - - + -
237G ILE* 1.3 94.7 - - + +
239G ILE* 1.3 63.2 + - - +
240G SER 3.8 0.2 - - - -
451G VAL* 4.6 10.1 - - + -
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Residues in contact with ILE 239 (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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77G ILE* 3.0 40.4 - - + +
79G ILE* 4.3 3.4 - - + -
170G ILE* 3.6 33.9 - - + -
173G MET* 4.4 10.1 - - - -
174G THR* 4.0 20.6 - - + -
223G VAL* 4.1 1.6 - - - -
224G TYR* 2.6 39.8 + - + -
225G GLY 2.5 18.6 + - - +
227G THR* 4.1 20.4 - - + -
237G ILE 4.3 4.7 - - - +
238G PRO* 1.3 76.5 - - - +
240G SER* 1.3 55.1 + - - +
241G GLY 3.5 12.6 - - - +
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Residues in contact with SER 240 (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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76G ALA* 3.4 10.5 - - - +
77G ILE 3.2 2.4 + - - -
221G SER* 3.5 5.2 - - - -
222G GLU 2.6 37.0 + - - +
223G VAL* 4.0 8.7 - - - +
224G TYR* 3.3 3.1 - - - -
238G PRO 3.8 1.0 - - - -
239G ILE* 1.3 71.7 - - - +
241G GLY* 1.3 56.4 - - - +
446G LEU 3.7 2.9 - - - +
447G ALA* 2.8 43.7 + - - +
450G ALA* 3.7 7.8 - - - +
451G VAL* 4.2 15.9 - - - -
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Residues in contact with GLY 241 (chain G).
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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77G ILE 3.4 5.1 + - - -
78G GLY* 3.9 6.1 - - - -
79G ILE* 3.0 25.0 + - - +
220G SER 4.1 5.2 - - - -
224G TYR* 3.5 2.6 - - - -
239G ILE* 3.5 4.2 - - - +
240G SER* 1.3 81.9 + - - +
242G ILE* 1.3 73.3 + - - +
443G ALA* 4.7 0.9 - - - -
446G LEU* 4.3 4.0 - - - -
447G ALA* 4.1 14.1 - - - +
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Residues in contact with ILE 242 (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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79G ILE* 3.4 16.1 + - + +
166G ASP* 3.9 24.0 - - + +
170G ILE* 4.1 24.0 - - + -
180G VAL* 4.5 8.7 - - + +
181G THR 4.6 0.9 - - - -
182G ASP* 3.0 50.9 - - + +
185G ASN* 4.0 3.1 - - - +
220G SER* 3.2 18.1 + - - +
224G TYR* 3.8 29.6 + - + +
241G GLY* 1.3 84.2 - - - +
243G ALA* 1.3 71.8 + - - +
443G ALA* 5.9 0.6 - - - +
446G LEU* 4.8 2.7 - - - +
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Residues in contact with ALA 243 (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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79G ILE 3.1 7.1 + - - +
80G THR* 2.8 26.7 - - - +
81G ASN* 3.6 5.7 + - - +
182G ASP* 3.7 3.1 - - - +
184G THR* 3.1 14.4 - - + +
185G ASN* 3.9 4.5 - - - -
220G SER* 4.4 3.1 - - - -
242G ILE* 1.3 80.0 - - - +
244G GLY* 1.3 64.7 + - - +
247G GLN* 4.8 3.1 - - + -
248G ALA* 4.5 12.1 - - + +
292G CYS* 5.0 2.7 - - - -
443G ALA* 6.0 1.3 - - - +
446G LEU* 3.7 23.3 - - + -
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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