Contacts of the strand formed by residues 193 - 199 (chain B) in PDB entry 2NUE
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 TYR 193 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163B ARG* 4.9 9.7 + - - -
164B TRP* 4.8 13.0 - + - -
188B ALA 3.8 0.2 - - - +
189B LYS* 3.2 4.9 - - - -
190B ILE* 3.1 39.1 + - + +
191B LYS* 3.4 8.1 + - + -
192B GLU* 1.3 93.7 - - + +
194B ARG* 1.3 63.1 + - - +
213B LEU* 3.5 22.2 - - + +
216B LEU* 4.5 27.6 - - + -
217B LEU* 4.0 24.0 - - + -
220B SER 5.8 3.6 - - - -
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Residues in contact with ARG 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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171B ARG* 6.0 1.4 - - - +
187B GLU* 3.7 24.1 + - + -
188B ALA 3.2 7.2 - - - +
189B LYS* 3.9 37.3 - - + +
191B LYS 5.4 0.2 + - - -
192B GLU* 5.0 9.6 + - - -
193B TYR* 1.3 82.1 - - - +
195B THR* 1.3 72.9 + - - +
196B LEU* 5.3 3.6 - - + -
213B LEU* 4.5 0.4 - - - +
216B LEU* 3.6 6.7 - - - +
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Residues in contact with THR 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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187B GLU* 3.4 9.0 - - - +
188B ALA* 3.1 33.2 + - - +
194B ARG* 1.3 85.2 - - - +
196B LEU* 1.3 70.7 + - - +
209B ALA 2.5 28.2 + - - -
212B GLU* 3.9 15.7 - - + -
213B LEU* 3.8 19.1 - - + +
216B LEU* 3.3 24.7 - - + -
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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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173B ILE* 3.6 31.6 - - + -
185B ILE* 4.5 12.6 - - + -
186B VAL 3.6 11.0 - - - +
187B GLU* 4.0 6.1 - - + -
194B ARG* 5.3 2.5 - - + -
195B THR* 1.3 89.2 - - - +
197B GLY* 1.3 59.4 + - - +
208B ARG* 4.6 1.2 - - - +
209B ALA* 3.7 12.8 + - - -
212B GLU* 4.7 9.4 - - - +
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Residues in contact with GLY 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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185B ILE* 3.4 8.0 - - - +
186B VAL 3.2 29.0 + - - -
196B LEU* 1.3 78.6 - - - +
198B GLU* 1.3 61.2 + - - -
205B ALA* 3.5 24.3 - - - +
208B ARG* 3.7 13.5 - - - -
209B ALA* 3.8 1.5 - - - +
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Residues in contact with GLU 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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212A GLU* 4.1 14.1 - - - +
215A LYS* 3.6 30.4 - - - +
183B LYS* 3.4 42.9 - - + +
184B PHE 3.4 5.8 - - - +
185B ILE* 4.8 4.9 - - + +
197B GLY* 1.3 72.4 - - - -
199B GLY* 1.3 64.0 + - - +
204B GLU* 4.2 1.6 - - - +
205B ALA* 4.1 1.6 - - - -
208B ARG* 2.9 47.6 + - - +
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Residues in contact with GLY 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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183B LYS* 3.5 5.9 - - - -
184B PHE 2.7 40.6 + - - +
198B GLU* 1.3 79.4 - - - +
200B LYS* 1.3 59.2 + - - -
201B SER 3.0 9.1 + - - +
204B GLU* 3.1 14.6 - - - -
205B ALA* 3.8 15.0 - - - +
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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