Contacts of the strand formed by residues 188 - 198 (chain B) in PDB entry 5NXR
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 VAL 188 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183B GLU* 3.4 3.8 - - - +
184B LEU* 3.0 52.5 + - + -
185B GLY 2.9 13.4 + - - +
186B TRP* 4.0 9.0 - - + +
187B GLY* 1.3 80.8 - - - +
189B THR* 1.3 73.0 + - - +
190B LEU* 4.4 9.0 - - + -
231B LYS 3.4 6.7 - - - +
232B PHE* 4.0 13.7 - - + -
403B LDA 4.4 28.0 - - + -
408B LDA 4.2 20.6 - - + -
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Residues in contact with THR 189 (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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107B TRP* 3.6 28.7 - - + -
181B ALA* 4.2 6.7 - - + -
182B TYR 3.3 17.3 - - - +
183B GLU* 3.8 22.0 + - + +
187B GLY 5.1 1.6 + - - -
188B VAL* 1.3 78.1 + - - +
190B LEU* 1.3 67.5 + - - +
230B GLY* 3.2 4.7 - - - -
231B LYS* 3.0 56.6 + - - +
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Residues in contact with LEU 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B TRP* 3.7 3.4 - - - -
181B ALA* 3.3 3.5 - - - +
182B TYR* 2.8 36.9 + - + +
184B LEU* 3.7 33.0 - - + +
188B VAL* 4.4 10.8 - - + -
189B THR* 1.3 81.9 - - - +
191B GLY* 1.3 59.3 + - - +
229B GLY 3.6 4.9 - - - +
230B GLY* 4.1 12.3 - - - -
403B LDA 5.5 5.6 - - + -
408B LDA 5.4 8.5 - - + -
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Residues in contact with GLY 191 (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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104B THR* 4.0 6.1 - - - -
107B TRP* 3.6 10.6 - - - -
180B THR* 3.1 14.1 - - - -
181B ALA* 4.1 0.7 - - - -
190B LEU* 1.3 76.7 - - - +
192B GLY* 1.3 58.4 + - - -
228B VAL* 3.5 8.5 - - - +
229B GLY 2.8 33.9 + - - +
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Residues in contact with GLY 192 (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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104B THR* 3.3 13.5 + - - -
178B PHE* 5.2 1.7 - - - -
179B SER* 3.3 2.8 - - - -
180B THR* 2.9 38.1 + - - +
191B GLY* 1.3 75.7 - - - -
193B GLY* 1.3 59.0 + - - -
227B ASN 3.1 14.1 - - - -
228B VAL* 4.1 2.7 - - - -
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Residues in contact with GLY 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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100B VAL 4.7 5.2 - - - -
101B VAL* 4.9 4.5 - - - -
104B THR* 4.5 0.9 - - - -
178B PHE* 3.2 13.9 - - - -
179B SER* 3.9 6.7 - - - -
192B GLY* 1.3 74.6 - - - -
194B TYR* 1.3 60.6 + - - +
226B TRP* 3.2 6.2 - - - +
227B ASN* 2.9 40.6 + - - +
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Residues in contact with TYR 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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100B VAL* 4.3 1.4 - - - +
101B VAL* 4.0 4.5 - - - +
176B TYR* 4.8 11.7 + + - -
177B GLY* 3.1 3.6 - - - -
178B PHE* 2.8 62.6 + + + +
193B GLY* 1.3 74.6 - - - +
195B SER* 1.3 78.2 + - - +
196B SER* 3.5 20.9 + - - -
224B GLN* 3.2 38.2 + - + -
225B ALA 3.5 5.8 - - - -
226B TRP* 3.7 22.2 - + + -
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Residues in contact with SER 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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101B VAL* 3.6 19.6 - - - +
125B PHE* 5.1 3.5 - - - +
126B MET* 3.7 27.7 + - - +
176B TYR 3.3 12.6 - - - -
177B GLY* 3.8 3.4 - - - -
194B TYR* 1.3 80.9 - - - +
196B SER* 1.3 62.0 + - - +
197B SER* 4.5 1.9 + - - -
223B ALA 5.1 0.7 + - - -
224B GLN* 3.4 11.1 - - - +
225B ALA* 2.8 38.6 + - - +
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Residues in contact with SER 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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175B GLY* 3.3 1.4 - - - -
176B TYR* 2.8 56.9 + - - +
194B TYR* 3.5 21.9 + - - -
195B SER* 1.3 74.9 - - - +
197B SER* 1.3 60.9 + - - +
222B ARG* 2.5 34.7 + - - +
223B ALA 3.6 6.0 + - - -
224B GLN* 4.6 5.8 + - - +
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Residues in contact with SER 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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125B PHE* 3.5 31.7 - - - +
126B MET* 3.2 26.3 - - - +
155B GLN* 4.8 0.5 + - - -
173B GLY 4.4 2.0 - - - -
174B ASP 3.4 13.0 - - - -
175B GLY* 3.4 3.0 - - - -
195B SER* 4.5 2.1 + - - -
196B SER* 1.3 77.7 + - - +
198B SER* 1.3 59.6 + - - +
222B ARG* 3.5 13.6 - - - +
223B ALA 2.8 35.5 + - - +
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Residues in contact with SER 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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125B PHE* 3.7 7.1 - - - -
173B GLY* 3.0 22.7 + - - -
174B ASP* 2.8 30.4 + - - +
197B SER* 1.3 78.3 - - - +
199B ARG* 1.3 66.7 + - - +
221B LYS 3.9 8.1 - - - -
222B ARG* 3.3 18.2 - - - +
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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