Contacts of the strand formed by residues 96 - 101 (chain C) 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 PHE 96 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95C PRO* 1.3 74.7 - - - +
97C LEU* 1.3 65.1 + - - +
119C ALA* 3.5 22.9 - - + -
120C GLY 3.9 15.9 - - - +
121C VAL* 3.5 14.6 - - + +
122C HIS* 3.0 45.8 + - + +
187C MSE 6.2 0.2 - - + -
191C LEU* 3.4 17.0 - - + -
193C LEU* 5.6 1.6 - - + -
235C LEU* 4.0 29.4 - - + -
238C ALA* 3.7 31.2 - - + -
239C VAL* 4.6 3.4 - - + -
242C ARG* 3.8 36.8 - - - +
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Residues in contact with LEU 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85C LEU* 5.6 2.5 - - + -
88C LEU* 6.1 1.3 - - + -
89C ILE* 4.4 10.1 - - + -
92C LEU* 5.1 5.4 - - + -
95C PRO* 4.6 5.6 - - + -
96C PHE* 1.3 90.1 - - - +
98C LEU* 1.3 61.7 - - - +
99C ILE* 5.4 0.7 - - + -
121C VAL* 4.4 3.5 - - - +
122C HIS* 4.2 9.2 - - + -
123C ALA* 3.7 30.3 - - + +
125C ILE* 4.4 16.4 - - + -
164C LEU* 4.2 30.1 - - + -
169C ILE* 4.2 16.8 - - + -
191C LEU 2.8 16.0 + - - +
192C ALA* 3.2 11.2 - - + -
193C LEU* 2.9 28.3 + - - +
235C LEU* 5.3 0.2 - - - +
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Residues in contact with LEU 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97C LEU* 1.3 75.9 - - - +
99C ILE* 1.3 62.0 + - - +
100C LEU* 3.9 26.9 - - + -
112C CYS* 4.1 9.6 - - + +
116C ALA* 4.0 15.5 - - + -
121C VAL* 4.0 17.7 - - + +
123C ALA 3.2 6.8 + - - +
124C VAL* 3.2 27.7 - - + +
125C ILE* 2.7 32.4 + - - +
193C LEU* 3.5 19.7 - - + +
195C MSE 4.1 13.9 - - + -
231C THR* 4.1 17.9 - - + -
235C LEU* 4.3 4.5 - - + -
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Residues in contact with ILE 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97C LEU* 5.4 0.4 - - + -
98C LEU* 1.3 78.2 - - - +
100C LEU* 1.3 70.1 + - - +
125C ILE* 3.4 28.0 - - + +
157C LEU* 4.0 25.1 - - + -
160C THR* 6.1 0.4 - - + -
161C MSE 4.1 18.6 - - + -
164C LEU* 4.0 25.4 - - + -
171C ILE* 4.9 2.5 - - + -
192C ALA* 4.3 15.0 - - + -
193C LEU 2.7 15.2 + - - +
194C VAL* 3.2 30.2 - - + -
195C MSE 2.9 25.8 + - - +
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Residues in contact with LEU 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98C LEU* 3.9 22.0 - - + -
99C ILE* 1.3 74.5 - - - +
101C ASP* 1.3 60.6 + - - +
102C GLY 3.4 2.0 + - - -
103C VAL* 3.9 25.7 + - + +
109C LEU* 4.2 17.9 - - + -
112C CYS* 3.9 37.5 - - + -
124C VAL* 3.7 26.5 - - + -
125C ILE 3.0 8.9 + - - +
126C VAL* 4.0 9.7 - - + +
127C PRO* 3.2 25.1 - - - +
195C MSE 3.6 20.4 - - + -
231C THR* 4.3 0.7 - - - +
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Residues in contact with ASP 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99C ILE 4.0 0.8 + - - -
100C LEU* 1.3 71.4 - - - +
102C GLY* 1.3 56.8 + - - +
103C VAL* 3.8 0.9 - - - +
130C ARG* 2.7 39.4 + - - +
157C LEU* 3.0 16.2 - - + +
194C VAL* 4.5 2.7 - - + -
195C MSE 2.8 17.0 + - - +
196C GLY* 4.4 0.7 - - - -
197C ALA* 3.2 21.8 + - - +
201C GLY 3.8 3.1 - - - +
202C MSE 3.2 10.2 - - + -
203C ARG* 2.7 34.4 + - - +
206C THR* 3.0 21.6 + - + -
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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