Contacts of the strand formed by residues 161 - 166 (chain G) in PDB entry 3EXG
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 CYS 161 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84G HIS 3.2 11.2 - - - +
85G LEU 4.8 0.4 - - - -
86G ILE* 4.8 1.3 - - - -
145G GLY* 3.6 22.7 - - - -
148G ILE* 3.9 24.0 - - + -
149G ALA* 4.0 20.2 - - + +
152G CYS* 4.7 0.7 - - - -
160G VAL* 1.3 78.1 - - - +
162G LEU* 1.3 72.2 + - - +
163G THR* 3.8 12.3 + - - -
188G PRO 3.0 11.9 + - - +
189G CYS* 3.5 1.8 - - - -
190G ILE* 2.8 28.8 + - - +
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Residues in contact with LEU 162 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75G LEU* 3.9 17.0 - - + -
79G ILE* 3.9 36.6 - - + -
83G ASP* 5.3 0.7 - - + -
84G HIS 2.8 11.2 + - - +
85G LEU* 3.4 29.4 - - + +
86G ILE* 2.9 29.1 + - - +
160G VAL* 4.2 9.9 - - + +
161G CYS* 1.3 76.3 - - - +
163G THR* 1.3 60.6 + - - +
164G LEU* 3.9 0.7 - - - -
190G ILE* 3.7 30.3 - - + -
192G ILE* 3.5 27.1 - - + -
237G THR* 4.7 3.6 - - + -
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Residues in contact with THR 163 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86G ILE* 3.6 6.5 - - + -
141G GLN* 3.7 9.9 - - + +
142G VAL* 3.6 44.9 - - + +
145G GLY* 3.3 23.4 - - - -
161G CYS* 3.8 2.8 + - - -
162G LEU* 1.3 72.7 - - - +
164G LEU* 1.3 60.0 + - - +
165G TYR* 4.2 2.8 - - - -
189G CYS* 3.5 23.2 - - - -
190G ILE 3.1 7.6 + - - -
191G PHE* 3.5 5.2 - - + -
192G ILE* 2.8 30.4 + - - +
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Residues in contact with LEU 164 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71G CYS* 6.0 0.2 - - + -
75G LEU* 4.0 10.5 - - + -
85G LEU* 3.8 32.8 - - + -
86G ILE 2.9 18.3 + - - +
87G THR* 3.5 18.8 - - - +
88G ALA 4.1 0.2 + - - -
94G PHE* 3.1 30.5 - - + -
141G GLN* 3.0 25.6 + - - +
162G LEU 4.2 0.9 - - - +
163G THR* 1.3 73.8 - - - +
165G TYR* 1.3 61.8 + - - +
192G ILE* 3.1 29.8 - - + +
194G GLU* 3.6 28.7 - - + +
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Residues in contact with TYR 165 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87G THR* 5.7 0.2 - - - -
88G ALA* 5.4 1.3 - - - +
139G GLY* 5.5 0.2 - - - -
141G GLN* 3.5 16.8 - - - +
142G VAL* 3.7 26.2 - - + -
163G THR 4.2 3.8 - - - -
164G LEU* 1.3 76.8 - - - +
166G GLY* 1.3 73.8 + - - +
169G ALA* 4.4 8.7 - - + -
170G ALA* 4.1 11.7 - - + -
175G ILE* 3.7 23.1 - - + -
179G TYR* 2.5 29.3 + - - -
191G PHE* 4.3 17.7 + + + +
192G ILE 3.0 13.0 + - - -
193G CYS* 3.3 36.2 + - + +
194G GLU* 2.9 29.9 + - - -
213G TYR* 5.0 1.2 + - - +
252G LEU* 4.2 10.9 - - - +
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Residues in contact with GLY 166 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88G ALA* 5.5 4.8 - - - +
141G GLN* 4.9 0.8 - - - +
165G TYR* 1.3 92.3 - - - +
167G ASP* 1.3 60.4 + - - -
168G GLY 3.1 4.3 - - - -
169G ALA* 2.9 22.9 + - - +
170G ALA 3.5 0.7 + - - -
193G CYS* 4.4 0.9 - - - -
194G GLU* 3.7 12.3 + - - -
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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