Contacts of the helix formed by residues 165 - 175 (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 VAL 165 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11G GLN* 3.1 33.2 - - + +
52G ILE* 4.2 16.8 - - + -
81G ASN* 3.8 21.9 + - + +
82G GLN* 4.3 13.4 + - + +
85G THR* 3.7 25.0 + - - +
87G ILE* 5.4 8.3 - - + -
164G THR* 1.3 76.7 - - - +
166G ASP* 1.3 50.7 + - - +
168G TRP* 4.3 6.1 - - + -
169G LEU* 2.5 55.2 + - + +
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Residues in contact with ASP 166 (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* 4.2 17.9 - - + -
81G ASN* 3.4 15.5 + - - +
164G THR* 2.3 29.6 + - - -
165G VAL* 1.3 69.0 - - - +
167G THR* 1.3 61.8 + - - -
169G LEU* 3.7 1.0 - - - +
170G ILE* 2.7 41.6 + - - +
180G VAL 4.4 0.7 - - - -
181G THR* 2.6 35.1 + - - -
182G ASP 3.2 7.8 + - - -
185G ASN* 3.2 22.6 - - - +
242G ILE* 3.9 14.8 - - + +
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Residues in contact with THR 167 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89G TRP* 3.8 5.2 - - + -
162G PHE 3.7 7.4 - - - +
163G GLY* 3.6 19.7 - - - -
164G THR 3.1 14.3 + - - -
166G ASP* 1.3 83.0 + - - +
168G TRP* 1.3 64.2 + - - +
170G ILE* 3.7 1.0 - - - +
171G TRP* 3.1 24.4 + - - +
178G VAL 5.1 0.5 - - - +
179G HIS* 3.8 20.4 - - + +
180G VAL 2.7 27.7 + - - +
181G THR* 3.1 22.0 - - - -
215G PRO* 3.6 5.7 - - + +
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Residues in contact with TRP 168 (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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49G PRO* 3.5 37.8 + - + +
50G MET* 4.2 14.1 - - - -
52G ILE* 4.8 7.4 - - + +
53G TRP* 3.9 15.2 - + + +
87G ILE* 3.8 24.8 - - + +
89G TRP* 3.7 60.8 - + + -
94G GLY 4.0 18.6 - - - -
96G PRO* 4.2 9.9 - - + -
164G THR 2.7 20.3 + - - +
165G VAL* 3.8 10.5 - - + +
167G THR* 1.3 72.4 - - - +
169G LEU* 1.3 80.2 + - + +
171G TRP* 4.3 2.6 - + - +
172G LYS* 3.1 47.4 + - + +
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Residues in contact with LEU 169 (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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9G LEU* 5.2 6.3 - - + -
11G GLN* 3.8 20.9 - - + +
52G ILE* 5.3 1.1 - - + -
53G TRP* 4.1 23.6 - - + -
56G GLN* 3.6 39.7 - - + +
79G ILE* 4.4 20.6 - - + -
80G THR 5.3 2.2 - - - +
81G ASN* 5.5 0.7 - - + -
165G VAL* 2.5 34.6 + - + +
166G ASP* 3.7 5.8 - - - +
168G TRP* 1.3 81.3 - - + +
170G ILE* 1.3 55.6 + - - +
172G LYS* 3.5 2.7 + - - +
173G MET* 2.8 38.8 + - + +
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Residues in contact with ILE 170 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79G ILE* 4.0 11.7 - - + -
166G ASP 2.7 24.1 + - - +
167G THR* 3.7 4.9 - - - +
169G LEU* 1.3 68.7 - - - +
171G TRP* 1.3 56.3 + - - +
173G MET* 2.4 34.7 + - - +
174G THR* 3.1 12.8 + - + -
178G VAL* 3.3 37.2 - - + +
180G VAL* 4.3 4.5 - - + +
224G TYR* 4.6 13.5 - - + -
239G ILE* 3.6 42.8 - - + -
242G ILE* 4.1 18.6 - - + -
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Residues in contact with TRP 171 (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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89G TRP* 3.5 28.9 - + + -
91G LYS* 3.3 29.7 - - + +
92G GLU 5.3 0.9 - - - -
93G THR 5.0 0.2 - - - -
94G GLY* 3.5 28.5 - - - -
161G LEU* 3.0 27.8 - - + +
167G THR 3.1 16.2 + - - +
168G TRP* 4.3 3.6 - + - +
170G ILE* 1.3 76.0 - - - +
172G LYS* 1.3 89.5 + - + +
173G MET 3.1 0.9 + - - -
174G THR* 3.5 3.8 - - - -
175G GLN 3.5 4.0 + - - -
176G GLY* 2.9 56.6 + - - -
178G VAL 3.2 23.8 - - - +
179G HIS* 4.1 13.2 - - + +
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Residues in contact with LYS 172 (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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50G MET* 5.2 3.8 - - - +
53G TRP* 3.3 58.6 - - + +
93G THR 5.3 1.4 + - - -
94G GLY* 3.7 25.0 + - - +
168G TRP* 3.1 43.2 + - + +
169G LEU* 4.2 2.9 - - - +
170G ILE 2.9 0.4 + - - -
171G TRP* 1.3 98.7 - - + +
173G MET* 1.3 59.0 + - - +
175G GLN* 4.4 6.0 + - - +
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Residues in contact with MET 173 (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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9G LEU* 4.3 20.0 - - + -
53G TRP* 5.2 16.8 - - + -
57G SER* 6.4 1.6 - - - -
60G LEU* 4.4 14.4 - - + -
77G ILE* 5.2 4.5 - - + -
79G ILE* 4.0 24.9 - - - -
169G LEU* 2.8 30.1 - - + +
170G ILE* 2.4 24.5 + - - +
172G LYS* 1.3 67.7 - - - +
174G THR* 1.3 49.3 + - - +
175G GLN* 2.8 18.9 + - - +
227G THR* 2.7 42.6 + - + +
228G ASN* 4.7 6.6 + - - -
239G ILE* 4.4 15.0 - - + -
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Residues in contact with THR 174 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170G ILE* 3.7 14.6 - - + +
171G TRP* 3.5 7.1 - - - -
173G MET* 1.3 71.9 - - - +
175G GLN* 1.3 50.1 + - - +
176G GLY 2.4 2.1 + - - -
177G ARG* 2.4 44.5 + - - +
178G VAL* 2.9 55.3 + - + +
225G GLY* 5.1 0.9 - - - +
226G GLN 4.1 18.8 - - - +
239G ILE* 4.0 20.0 - - + -
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Residues in contact with GLN 175 (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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171G TRP* 3.5 6.9 + - - -
172G LYS 4.6 5.4 - - - +
173G MET 2.8 11.1 + - - +
174G THR* 1.3 72.9 - - - +
176G GLY* 1.3 54.1 + - - +
177G ARG* 3.3 2.0 + - - -
228G ASN* 6.1 2.5 - - - +
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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