Contacts of the strand formed by residues 191 - 196 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95D PRO 2.7 16.1 + - - +
96D PHE* 3.9 25.6 - - + -
97D LEU* 2.7 33.1 + - - +
169D ILE* 3.7 3.5 - - - +
170D TRP* 3.4 15.0 - - + +
172D VAL* 3.5 32.5 - - + -
186D LYS 4.2 3.1 - - - +
187D MSE 3.2 52.3 - - + +
188D THR 4.7 2.0 - - - +
189D GLY 3.3 0.6 + - - +
190D ARG* 1.3 74.3 - - - +
192D ALA* 1.3 62.0 + - - +
193D LEU* 4.5 3.8 - - + +
238D ALA* 4.1 1.8 - - + -
242D ARG* 3.8 13.7 - - - +
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Residues in contact with ALA 192 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97D LEU* 3.1 18.6 - - + -
99D ILE* 4.5 7.6 - - + -
164D LEU* 4.2 13.5 - - + -
169D ILE* 3.9 14.8 - - + -
170D TRP 2.9 5.9 + - - +
171D ILE* 3.4 20.2 - - + +
172D VAL* 2.9 27.4 + - - +
191D LEU* 1.3 76.5 - - - +
193D LEU* 1.3 61.3 + - - +
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Residues in contact with LEU 193 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96D PHE* 5.2 1.8 - - + -
97D LEU 2.6 13.8 + - - +
98D LEU* 3.4 10.8 - - + +
99D ILE* 2.7 33.4 + - - +
172D VAL* 3.4 20.4 - - + +
174D THR* 4.4 6.7 - - - +
187D MSE 4.4 19.5 - - - -
191D LEU* 4.2 10.2 - - + +
192D ALA* 1.3 73.7 - - - +
194D VAL* 1.3 56.7 + - - +
195D MSE 4.0 17.7 - - + -
214D ILE* 4.5 2.5 - - + -
231D THR 4.6 1.3 - - - +
234D CYS* 3.8 33.2 - - + +
235D LEU* 3.4 34.1 - - + +
238D ALA* 6.0 0.4 - - + -
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Residues in contact with VAL 194 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99D ILE* 3.3 29.2 - - + +
101D ASP* 4.8 2.5 - - + -
161D MSE 4.0 11.0 - - + -
171D ILE* 3.5 30.5 - - + -
172D VAL 2.7 14.1 + - - +
173D GLY* 3.6 6.2 - - - -
174D THR* 3.0 32.2 + - - +
193D LEU* 1.3 78.4 - - - +
195D MSE 1.3 67.8 - - - +
196D GLY 4.4 0.2 + - - -
202D MSE 3.6 25.0 - - + +
206D THR* 3.9 14.8 - - + -
210D CYS* 4.3 1.6 - - - -
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Residues in contact with MSE 195 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98D LEU* 3.9 21.5 - - + -
99D ILE 2.9 6.5 + - - -
100D LEU* 3.5 16.7 - - + +
101D ASP* 2.8 27.5 + - - +
103D VAL* 5.2 0.4 - - - +
174D THR* 3.3 36.6 - - + +
193D LEU* 4.0 18.4 - - - -
194D VAL* 1.3 81.6 - - - +
196D GLY* 1.3 65.6 + - - +
202D MSE 4.6 0.4 - - - -
227D VAL* 4.6 4.0 - - + +
230D ALA* 3.4 20.4 - - + +
231D THR* 3.4 44.0 - - + +
234D CYS* 4.0 7.9 - - - -
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Residues in contact with GLY 196 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101D ASP 3.2 8.7 - - - -
103D VAL* 5.0 1.3 - - - -
174D THR* 4.9 7.6 + - - +
195D MSE 1.3 78.7 - - - +
197D ALA* 1.3 69.2 + - - +
198D GLU* 3.6 1.4 + - - -
201D GLY* 3.7 18.8 - - - -
202D MSE 3.8 10.3 - - - +
227D VAL* 3.6 15.6 - - - +
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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