Contacts of the strand formed by residues 192 - 199 (chain B) in PDB entry 7NPA
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 LYS 192 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151B GLU* 3.0 19.9 + - + +
152B LYS* 3.4 17.5 - - + +
153B VAL* 3.0 25.6 + - - +
190B LEU 3.9 0.8 + - - -
191B PRO* 1.3 71.0 - - - +
193B ILE* 1.3 66.2 - - - +
194B GLU* 2.6 36.7 + - - +
289B LYS* 4.6 6.6 - - - +
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Residues in contact with ILE 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142B LEU* 4.2 13.7 - - + -
153B VAL* 3.7 8.7 - - + +
155B VAL* 3.9 14.1 - - + -
165B LEU* 3.5 42.6 - - + +
168B LEU* 4.2 15.7 - - + -
169B GLN* 3.0 33.4 + - + +
191B PRO 3.4 8.9 + - - +
192B LYS* 1.3 77.8 - - - +
194B GLU* 1.3 60.2 + - - +
195B TYR 3.8 12.1 - - - +
196B LEU* 3.7 30.3 - - + -
289B LYS* 5.1 1.2 + - - -
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Residues in contact with GLU 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B LYS 4.1 8.4 - - - +
102B ILE* 4.5 0.7 - - + -
152B LYS* 3.8 34.4 + - + +
153B VAL 2.8 13.4 + - - +
169B GLN* 5.3 1.3 - - - -
192B LYS* 2.6 38.6 + - - +
193B ILE* 1.3 73.4 - - - +
195B TYR* 1.3 83.6 + - + +
268B ASP* 4.1 2.2 - - - +
289B LYS* 2.8 55.2 + - - +
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Residues in contact with TYR 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B PHE* 4.3 7.6 - + - -
96B LEU* 3.7 25.1 - - + -
101B LYS* 3.5 18.8 - - - +
102B ILE* 3.5 26.5 - - + -
153B VAL 3.5 2.2 + - - -
154B ALA* 3.4 13.4 - - + -
155B VAL 2.9 26.0 + - - -
193B ILE* 3.5 7.9 - - - +
194B GLU* 1.3 102.5 + - + +
196B LEU* 1.3 63.5 - - - +
197B ILE* 4.0 7.9 - - + -
268B ASP* 3.5 7.0 - - + +
289B LYS* 3.7 36.6 - - + +
292B GLU* 2.5 38.7 + - - -
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Residues in contact with LEU 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155B VAL* 3.6 6.3 - - + -
162B ILE* 4.0 24.2 - - + +
165B LEU* 3.7 40.2 - - + -
166B ARG* 3.7 40.4 - - + +
169B GLN* 3.7 19.5 - - - +
193B ILE* 3.7 16.8 - - + -
195B TYR* 1.3 74.9 - - - +
197B ILE* 1.3 61.9 + - - +
267B ALA* 3.6 1.6 - - - +
268B ASP* 2.9 50.6 + - - +
269B VAL 3.5 2.6 + - - -
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Residues in contact with ILE 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B VAL* 4.2 32.1 - - + -
92B PHE* 3.8 25.8 - - + -
93B LEU* 3.6 33.4 - - + -
96B LEU* 4.7 1.3 - - + -
154B ALA* 4.5 11.2 - - + -
155B VAL 2.9 11.5 + - - +
156B VAL* 3.2 12.7 - - + +
157B GLY 3.0 25.1 + - - -
162B ILE* 4.0 2.0 - - - -
195B TYR* 4.8 3.1 - - + -
196B LEU* 1.3 74.8 - - - +
198B GLY* 1.3 64.9 + - - +
268B ASP* 6.1 0.2 - - + -
269B VAL* 3.4 24.2 - - + +
271B VAL* 4.4 7.9 - - + -
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Residues in contact with GLY 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157B GLY 3.3 7.6 - - - -
162B ILE* 3.8 7.4 - - - -
197B ILE* 1.3 75.9 - - - +
199B LEU* 1.3 63.9 + - - +
264B ALA* 3.7 22.0 - - - -
267B ALA* 3.5 6.3 - - - +
269B VAL 2.9 10.1 + - - +
270B SER* 3.2 1.7 - - - -
271B VAL* 2.8 28.1 + - - +
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Residues in contact with LEU 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B VAL* 4.1 20.9 - - + -
132B SER* 5.4 9.6 - - - +
156B VAL* 4.1 25.8 - - + -
157B GLY 2.9 17.4 + - - +
158B LEU* 4.1 22.2 - - + -
159B PRO* 3.1 26.5 - - - +
197B ILE 5.2 0.2 - - - +
198B GLY* 1.3 77.9 - - - +
200B LEU* 1.3 72.7 + - - +
264B ALA* 3.8 3.0 - - - +
271B VAL* 3.4 9.9 - - + +
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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