Contacts of the strand formed by residues 191 - 196 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95A PRO 2.9 13.4 + - - +
96A PHE* 3.4 31.1 - - + -
97A LEU* 2.6 32.7 + - - +
169A ILE* 3.6 6.3 - - - +
170A TRP* 3.4 23.3 - - + +
172A VAL* 3.5 24.7 - - + -
186A LYS 4.3 2.7 - - - +
187A MSE 4.1 46.9 - - + +
188A THR 4.8 4.3 - - - +
189A GLY 3.1 2.6 + - - +
190A ARG* 1.3 75.2 - - - +
192A ALA* 1.3 62.1 + - - +
193A LEU* 4.8 2.7 - - + +
238A ALA* 4.5 0.2 - - + -
242A ARG* 4.0 12.3 - - - +
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Residues in contact with ALA 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A LEU* 3.1 18.4 - - + +
99A ILE* 4.1 21.1 - - + -
164A LEU* 4.4 4.5 - - + -
169A ILE* 3.9 14.8 - - + -
170A TRP 2.9 8.2 + - - +
171A ILE* 3.6 11.9 - - + +
172A VAL* 3.0 28.4 + - - +
191A LEU* 1.3 77.6 - - - +
193A LEU* 1.3 59.4 + - - +
194A VAL* 4.0 0.8 + - - -
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Residues in contact with LEU 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A PHE* 5.7 1.1 - - + -
97A LEU 2.7 14.4 + - - +
98A LEU* 3.3 14.0 - - + +
99A ILE 2.7 27.7 + - - -
172A VAL* 3.4 13.0 - - + +
174A THR* 4.0 10.3 - - + -
187A MSE 4.2 19.3 - - + -
191A LEU* 4.6 5.1 - - + +
192A ALA* 1.3 71.9 - - - +
194A VAL* 1.3 64.1 + - - +
195A MSE 3.9 23.3 - - + -
214A ILE* 4.6 2.5 - - + -
231A THR 4.3 2.2 - - - +
234A CYS* 3.6 30.1 - - + -
235A LEU* 3.2 34.8 - - + +
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Residues in contact with VAL 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A ILE* 3.4 33.7 - - + +
101A ASP* 4.5 2.7 - - + -
161A MSE 4.4 3.1 - - + -
171A ILE* 3.6 31.4 - - + -
172A VAL 2.9 9.6 + - - +
173A GLY* 3.4 1.3 - - - -
174A THR* 3.1 27.5 + - - +
192A ALA 4.4 0.2 - - - +
193A LEU* 1.3 76.7 - - - +
195A MSE 1.3 73.1 + - - +
202A MSE 3.8 25.3 - - + +
206A THR* 3.9 14.8 - - + -
210A CYS* 4.1 8.1 - - - -
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Residues in contact with MSE 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A LEU* 4.2 18.4 - - + -
99A ILE 3.0 5.0 + - - +
100A LEU* 3.7 11.7 - - + +
101A ASP* 2.9 27.4 + - - +
103A VAL* 5.7 0.6 - - - +
174A THR* 3.5 40.2 - - + +
193A LEU* 3.9 17.7 - - - -
194A VAL* 1.3 78.6 - - - +
196A GLY* 1.3 65.0 + - - +
202A MSE 4.3 3.1 - - - -
216A ILE* 4.8 1.6 - - + -
227A VAL* 4.8 6.5 - - + +
230A ALA* 3.6 34.5 - - + +
231A THR* 3.4 31.6 - - - +
234A CYS* 4.2 4.0 - - - -
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Residues in contact with GLY 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A ASP 3.0 12.1 - - - -
102A GLY 5.3 0.2 - - - -
103A VAL* 5.5 2.5 - - - -
174A THR* 4.5 4.6 + - - -
195A MSE 1.3 78.2 - - - +
197A ALA* 1.3 71.0 + - - +
198A GLU* 3.7 0.5 + - - -
201A GLY* 3.6 2.4 - - - -
202A MSE 3.6 27.0 - - - +
227A VAL* 4.0 15.3 - - - +
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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