Contacts of the strand formed by residues 96 - 101 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95F PRO* 1.3 74.1 - - - +
97F LEU* 1.3 65.1 + - - +
119F ALA* 3.4 32.8 - - + -
120F GLY 3.9 12.6 - - - +
121F VAL* 3.4 8.8 - - + +
122F HIS* 2.8 50.2 + - + +
191F LEU* 3.5 28.7 - - + -
193F LEU* 5.4 2.0 - - + -
235F LEU* 4.0 30.7 - - + -
238F ALA* 3.8 23.6 - - + -
239F VAL* 4.3 5.8 - - + -
242F ARG* 3.7 27.6 - - + +
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Residues in contact with LEU 97 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85F LEU* 5.6 1.8 - - + -
88F LEU* 5.9 1.6 - - + -
89F ILE* 4.2 12.6 - - + -
92F LEU* 5.1 2.7 - - + -
95F PRO* 4.4 8.5 - - + -
96F PHE* 1.3 94.1 - - - +
98F LEU* 1.3 57.4 + - - +
99F ILE* 5.4 0.7 - - + -
121F VAL* 4.2 1.8 - - - -
122F HIS* 4.1 7.9 - - + -
123F ALA* 3.6 27.4 - - + +
125F ILE* 4.4 15.9 - - + -
164F LEU* 4.0 29.8 - - + -
169F ILE* 4.1 14.1 - - + -
191F LEU 2.8 17.6 + - - +
192F ALA* 3.1 10.6 - - + -
193F LEU* 2.8 33.2 + - - +
235F LEU* 5.4 0.2 - - - +
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Residues in contact with LEU 98 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97F LEU* 1.3 74.7 - - - +
99F ILE* 1.3 57.2 + - - +
100F LEU* 4.1 19.1 - - + -
112F CYS 4.2 5.8 - - - +
116F ALA* 3.8 25.4 - - + -
121F VAL* 3.8 17.7 - - + +
123F ALA 3.1 6.1 + - - +
124F VAL* 3.1 16.2 - - + +
125F ILE* 2.8 32.2 + - - +
193F LEU* 3.5 15.5 - - + +
195F MSE 4.1 14.4 - - + -
231F THR* 4.0 31.0 - - + -
235F LEU* 4.1 16.4 - - + -
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Residues in contact with ILE 99 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97F LEU* 5.4 0.9 - - + -
98F LEU* 1.3 78.6 - - - +
100F LEU* 1.3 70.8 + - - +
101F ASP 4.6 0.2 - - - +
125F ILE* 3.2 26.0 - - + +
157F LEU* 4.0 25.6 - - + -
160F THR* 6.3 0.4 - - + -
161F MSE 4.1 17.3 - - + -
164F LEU* 3.9 26.2 - - + -
171F ILE* 5.0 1.6 - - + -
192F ALA* 4.3 11.2 - - + -
193F LEU 2.7 15.3 + - - +
194F VAL* 3.4 32.0 - - + -
195F MSE 2.9 28.4 + - - +
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Residues in contact with LEU 100 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98F LEU* 4.1 15.3 - - + -
99F ILE* 1.3 80.9 - - - +
101F ASP* 1.3 60.5 + - - +
102F GLY 3.7 1.3 + - - -
103F VAL* 3.9 23.3 + - + -
109F LEU* 4.1 19.1 - - + -
112F CYS* 3.7 37.7 - - + -
113F LEU 5.6 0.2 - - - +
124F VAL* 4.0 23.6 - - + -
125F ILE 3.0 8.5 + - - -
126F VAL* 3.6 14.1 - - + +
127F PRO* 3.2 22.7 - - - +
131F SER* 4.9 1.0 + - - -
195F MSE 3.7 24.2 - - + -
227F VAL* 5.2 0.2 - - + -
231F THR* 4.4 0.4 - - - +
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Residues in contact with ASP 101 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99F ILE* 3.9 0.6 + - + -
100F LEU* 1.3 70.7 - - - +
102F GLY* 1.3 60.0 + - - +
103F VAL* 3.6 1.1 - - - +
127F PRO* 3.9 11.8 - - - +
130F ARG* 2.7 35.6 + - - -
157F LEU* 3.9 13.8 - - + +
194F VAL* 4.7 3.6 - - + -
195F MSE 2.9 15.8 + - - +
196F GLY* 3.4 3.2 - - - -
197F ALA 3.2 22.2 + - - -
201F GLY 4.2 0.7 - - - +
202F MSE 4.7 4.0 - - + -
203F ARG* 3.1 21.0 + - - +
206F THR* 2.6 37.2 + - + -
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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