Contacts of the strand formed by residues 161 - 168 (chain G) in PDB entry 2NN6
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 161 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A SER* 3.8 25.6 - - - +
8A ASN* 4.0 4.3 - - + +
9A CYS* 4.1 32.8 - - + +
117G ILE* 5.6 0.2 - - + -
118G GLY 2.8 7.9 - - - +
159G GLY 3.8 3.6 - - - +
160G ASP* 1.3 96.8 + - - +
162G ILE* 1.3 60.6 + - - +
191G VAL* 2.7 32.7 - - - +
192G ILE* 2.9 45.1 - - + -
198G LEU* 5.1 12.8 - - + -
237G TRP* 4.3 5.8 - - + -
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Residues in contact with ILE 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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116G VAL 3.6 0.9 - - - +
117G ILE* 3.1 8.3 - - - +
118G GLY* 2.6 53.2 + - - +
120G VAL* 3.4 29.4 - - + -
130G VAL* 3.7 15.7 - - + -
140G LEU* 5.2 4.5 - - + -
145G PHE* 5.0 3.4 - - + -
161G LEU* 1.3 82.0 - - - +
163G TYR* 1.3 75.7 + - - +
164G GLY* 3.9 1.3 + - - +
177G MET* 5.3 7.3 - - - +
179G CYS* 3.7 20.9 - - - -
191G VAL* 4.0 19.1 - - + +
192G ILE* 3.2 11.4 - - - +
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Residues in contact with TYR 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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115G HIS* 3.9 30.1 - - + +
116G VAL 3.6 16.4 - - - -
117G ILE* 4.4 1.6 - - + -
162G ILE* 1.3 85.4 - - - +
164G GLY* 1.3 59.9 + - - +
165G GLN* 4.2 1.7 + - - -
179G CYS* 3.8 2.1 - - - -
188G GLY 4.0 7.9 - - - -
189G MET* 2.9 61.0 - - + +
190G GLY 3.3 19.1 + - - +
192G ILE* 4.8 4.3 - - + -
229G VAL* 3.4 35.8 - - + +
230G PHE* 4.1 15.8 + - - +
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Residues in contact with GLY 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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114G ASP 3.3 1.2 - - - +
115G HIS* 3.7 1.0 - - - -
116G VAL* 3.0 37.7 + - - +
162G ILE* 3.9 1.2 - - - +
163G TYR* 1.3 77.1 - - - +
165G GLN* 1.3 65.7 + - - -
166G PHE* 4.2 1.0 + - - -
177G MET* 4.4 17.2 - - - +
178G VAL 3.2 13.7 - - - -
179G CYS* 4.8 0.9 - - - -
189G MET* 4.2 5.2 - - - -
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Residues in contact with GLN 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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113G GLY* 3.5 16.0 + - - -
114G ASP* 2.4 53.1 + - - +
115G HIS* 2.9 24.2 + - - +
163G TYR* 4.2 3.3 + - - -
164G GLY* 1.3 70.1 - - - -
166G PHE* 1.3 61.2 + - - +
167G VAL* 3.9 4.0 + - + +
177G MET* 4.0 0.7 - - - -
178G VAL* 2.9 30.0 + - - +
189G MET* 3.1 39.5 - - + +
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Residues in contact with PHE 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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108G TYR* 3.3 3.8 - + - -
110G PRO* 2.9 35.7 - - + -
111G VAL 3.1 26.9 - - - -
112G LYS 2.7 38.6 - - - +
113G GLY* 2.9 7.1 - - - -
114G ASP* 3.3 22.3 + - + -
116G VAL* 3.9 26.0 - - + -
132G VAL* 4.8 4.3 - - + -
164G GLY 5.0 0.9 - - - -
165G GLN* 1.3 73.9 - - - +
167G VAL* 1.3 56.4 + - - +
168G VAL 4.4 1.8 - - - +
169G ALA* 4.3 6.3 - - + -
175G PRO* 5.2 3.8 - - + -
176G GLU 2.8 26.0 - - - +
177G MET* 3.3 28.7 - - + +
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Residues in contact with VAL 167 (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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111G VAL 5.0 0.3 - - - +
112G LYS* 4.8 8.7 - - - -
113G GLY* 4.5 9.4 - - - +
165G GLN* 3.9 3.8 + - + +
166G PHE* 1.3 75.4 - - - +
168G VAL* 1.3 81.8 + - + +
169G ALA 4.0 1.8 + - - -
176G GLU 3.5 0.8 + - - +
178G VAL* 4.4 23.6 - - + -
182G SER* 5.4 7.9 - - - +
117I GLU* 6.0 0.7 - - - +
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Residues in contact with VAL 168 (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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166G PHE* 3.4 2.3 - - - +
167G VAL* 1.3 96.6 - - + +
169G ALA* 1.3 52.8 + - - +
170G ASN* 4.2 0.9 - - - -
173G MET* 4.0 16.2 - - + -
174G GLU 4.5 1.1 - - - -
175G PRO* 2.6 37.0 - - - +
176G GLU* 2.8 55.0 + - + +
80I SER* 3.9 21.3 - - - +
117I GLU* 4.9 10.5 - - - +
119I TYR* 5.8 4.3 - - + -
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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