Contacts of the strand formed by residues 96 - 101 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95E PRO* 1.3 71.3 - - - +
97E LEU* 1.3 64.3 + - - +
119E ALA* 3.4 26.2 - - + -
120E GLY 3.6 19.1 - - - +
121E VAL* 3.4 18.6 - - + +
122E HIS* 2.8 43.8 + - + -
191E LEU* 3.5 12.8 - - + -
193E LEU* 5.4 2.0 - - + -
235E LEU* 3.8 27.6 - - + -
238E ALA* 3.6 31.4 - - + -
239E VAL* 4.5 4.9 - - + -
242E ARG* 3.1 37.2 - - - +
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Residues in contact with LEU 97 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85E LEU* 5.8 1.1 - - + -
88E LEU* 5.4 2.7 - - + -
89E ILE* 5.0 8.3 - - + -
92E LEU* 5.1 4.0 - - + -
95E PRO* 4.5 7.4 - - + -
96E PHE* 1.3 88.3 - - - +
98E LEU* 1.3 57.4 + - - +
99E ILE* 5.4 0.2 - - + -
121E VAL* 4.4 2.7 - - - -
122E HIS* 4.3 9.0 - - + -
123E ALA* 3.7 29.4 - - + +
125E ILE* 4.4 14.4 - - + -
164E LEU* 3.8 27.1 - - + -
169E ILE* 3.7 29.2 - - + -
191E LEU 2.8 14.5 + - - +
192E ALA* 3.1 12.2 - - + -
193E LEU* 2.6 34.1 + - - +
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Residues in contact with LEU 98 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97E LEU* 1.3 74.8 - - - +
99E ILE* 1.3 63.4 + - - +
100E LEU* 3.8 34.5 - - + -
112E CYS* 4.3 4.9 - - + +
116E ALA* 4.2 21.3 - - + -
121E VAL* 3.9 19.0 - - + +
123E ALA 3.2 5.7 + - - -
124E VAL* 3.3 12.8 - - + +
125E ILE 2.9 24.9 + - - +
193E LEU* 3.3 28.7 - - + +
195E MSE 3.9 17.5 - - + -
231E THR* 3.8 18.2 - - + -
235E LEU* 4.2 5.4 - - + -
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Residues in contact with ILE 99 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97E LEU 5.4 0.4 - - - -
98E LEU* 1.3 77.3 - - - +
100E LEU* 1.3 71.0 + - - +
125E ILE* 3.4 26.5 - - + +
157E LEU* 3.7 34.3 - - + -
160E THR* 6.1 0.2 - - + -
161E MSE 4.2 18.4 - - + -
164E LEU* 4.0 24.7 - - + -
171E ILE* 5.1 1.1 - - + -
192E ALA* 4.3 10.8 - - + -
193E LEU 2.6 15.3 + - - +
194E VAL* 3.4 28.2 - - + -
195E MSE 2.9 27.5 + - - +
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Residues in contact with LEU 100 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98E LEU* 3.8 28.5 - - + -
99E ILE* 1.3 80.9 - - - +
101E ASP* 1.3 60.1 + - - +
102E GLY 3.4 2.5 + - - -
103E VAL* 3.6 23.5 + - + -
109E LEU* 4.3 20.2 - - + +
112E CYS* 3.6 35.9 - - + -
113E LEU* 5.5 0.7 - - + +
124E VAL* 4.3 18.4 - - + -
125E ILE 3.2 6.5 + - - -
126E VAL* 3.6 12.9 - - + +
127E PRO* 3.3 21.5 - - - +
131E SER* 4.6 0.2 + - - -
195E MSE 3.6 19.1 - - + -
231E THR* 4.4 0.2 - - - +
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Residues in contact with ASP 101 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99E ILE 4.0 0.6 - - - -
100E LEU* 1.3 71.9 - - - +
102E GLY* 1.3 67.5 + - - +
103E VAL* 3.5 0.8 - - - +
127E PRO* 4.0 10.3 - - - +
157E LEU* 3.5 16.5 - - + +
194E VAL* 4.8 3.1 - - + -
195E MSE 2.9 17.0 + - - +
196E GLY* 3.8 4.9 - - - -
197E ALA* 3.6 19.1 + - - +
201E GLY 4.1 5.2 - - - +
202E MSE 4.7 4.3 - - - -
203E ARG* 3.7 31.0 + - - +
206E THR* 2.3 43.6 + - + -
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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