Contacts of the strand formed by residues 191 - 196 (chain G) in PDB entry 1GZ0
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 LEU 191 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95G PRO 3.0 14.0 + - - +
96G PHE* 3.5 12.6 - - + -
97G LEU* 3.0 24.3 + - - +
169G ILE* 3.6 6.7 - - - +
170G TRP* 3.2 21.1 - - + +
172G VAL* 3.4 27.6 - - + -
186G LYS 4.3 2.7 - - - +
187G MSE 3.3 54.7 - - + +
189G GLY 2.8 12.7 + - - +
190G ARG* 1.3 74.8 - - - +
192G ALA* 1.3 69.1 + - - +
193G LEU* 4.3 1.8 - - + +
238G ALA* 4.1 10.8 - - + -
242G ARG* 4.2 7.0 - - - +
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Residues in contact with ALA 192 (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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97G LEU* 3.4 13.9 - - + +
99G ILE* 4.3 18.4 - - + -
164G LEU* 4.5 6.3 - - + -
169G ILE* 3.7 16.2 - - + -
170G TRP 2.7 11.0 + - - +
171G ILE* 3.3 16.6 - - + +
172G VAL* 2.8 28.9 + - - +
191G LEU* 1.3 79.5 - - - +
193G LEU* 1.3 59.8 + - - +
194G VAL* 3.9 0.4 + - - -
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Residues in contact with LEU 193 (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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96G PHE* 5.5 2.2 - - + -
97G LEU 2.9 11.0 + - - +
98G LEU* 3.5 10.4 - - + +
99G ILE* 2.7 32.2 + - - +
172G VAL 3.3 11.9 - - - +
174G THR* 4.0 18.4 - - - +
187G MSE 3.6 29.4 - - + -
191G LEU* 4.2 4.3 - - + +
192G ALA* 1.3 73.1 - - - +
194G VAL* 1.3 55.0 + - - +
195G MSE 4.0 13.5 - - - -
214G ILE* 4.3 6.1 - - + -
231G THR 4.5 1.1 - - - +
234G CYS* 3.6 27.6 - - + -
235G LEU* 3.5 32.8 - - + +
238G ALA* 6.1 0.7 - - + -
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Residues in contact with VAL 194 (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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99G ILE* 3.3 33.0 - - + +
101G ASP* 4.4 2.0 - - + -
161G MSE 4.2 3.1 - - + -
171G ILE* 3.4 33.7 - - + -
172G VAL 2.8 11.7 + - - +
173G GLY* 3.9 2.5 - - - -
174G THR* 3.0 27.7 + - - -
193G LEU* 1.3 76.3 - - - +
195G MSE 1.3 69.0 + - - +
196G GLY 4.4 0.2 + - - -
202G MSE 3.6 27.0 - - + +
206G THR* 3.9 15.9 - - + -
210G CYS* 4.1 5.2 - - - -
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Residues in contact with MSE 195 (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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98G LEU* 4.1 12.1 - - + -
99G ILE 2.8 6.9 + - - +
100G LEU* 3.6 12.3 - - + -
101G ASP* 2.9 27.0 + - - +
103G VAL* 5.5 0.4 - - - +
174G THR* 3.3 38.1 - - + +
193G LEU* 4.0 19.5 - - - -
194G VAL* 1.3 78.3 - - - +
196G GLY* 1.3 65.1 + - - +
202G MSE 5.2 0.9 - - - -
227G VAL* 4.6 4.9 - - + +
230G ALA* 3.7 19.1 - - + +
231G THR* 3.4 52.3 - - + +
234G CYS* 4.2 4.0 - - - -
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Residues in contact with GLY 196 (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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101G ASP* 4.3 6.7 - - - -
103G VAL* 4.9 4.7 - - - +
174G THR* 4.9 5.8 + - - -
194G VAL 4.4 0.2 + - - -
195G MSE 1.3 78.4 - - - +
197G ALA* 1.3 67.8 + - - +
198G GLU 3.8 0.3 + - - -
201G GLY* 3.7 18.4 - - - -
202G MSE 3.7 10.7 - - - +
227G VAL* 3.9 18.5 - - - +
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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