Contacts of the strand formed by residues 201 - 206 (chain B) in PDB entry 4NDH
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 HIS 201 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192B LYS* 3.7 6.2 - - - +
193B ASP* 2.9 47.5 + - + +
196B PRO* 3.5 23.7 - - + +
197B LYS* 3.0 30.0 + - + +
198B ALA 4.4 1.3 + - - +
199B ARG 4.2 0.4 - - - -
200B TYR* 1.3 76.3 - - - +
202B TRP* 1.3 78.2 + - - +
262B HIS* 2.9 24.0 + + + -
263B VAL 3.3 7.4 - - - -
264B ILE* 3.8 15.6 - - + +
282B PHE* 3.6 26.9 - + - -
401B AMP 4.3 1.8 - - - -
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Residues in contact with TRP 202 (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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182B VAL* 4.2 14.9 - - + +
190B VAL* 4.0 14.6 - - + -
191B ILE 3.4 15.0 - - - +
192B LYS* 3.9 27.1 - - + +
200B TYR* 3.7 31.9 - + + -
201B HIS* 1.3 82.6 - - - +
203B LEU* 1.3 66.1 + - - +
234B VAL* 3.5 27.1 - - + +
235B ILE* 4.4 8.1 - - + -
238B PHE* 3.6 26.2 - - + +
239B ALA* 3.9 13.7 - - + -
246B PHE* 3.7 24.9 - + - -
262B HIS* 3.6 4.2 - - - -
263B VAL* 2.9 55.4 + - + +
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Residues in contact with LEU 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B LEU* 4.1 13.2 - - + -
189B VAL 3.7 0.9 - - - +
190B VAL* 3.3 6.7 - - - +
191B ILE* 2.8 36.1 + - + +
193B ASP* 3.3 26.9 - - + +
201B HIS* 4.3 0.2 - - - +
202B TRP* 1.3 77.6 - - - +
204B VAL* 1.3 61.8 + - - +
205B LEU* 4.0 19.2 + - + +
260B HIS* 5.0 3.1 - - + -
261B LEU 3.3 4.3 - - - +
262B HIS* 3.4 33.7 - - + +
401B AMP 3.4 46.0 - - - +
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Residues in contact with VAL 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B VAL* 4.0 20.9 - - + -
189B VAL 3.6 4.3 - - - +
190B VAL* 4.1 14.4 - - + -
203B LEU* 1.3 74.4 - - - +
205B LEU* 1.3 62.3 + - - +
227B MET* 3.6 43.2 - - + +
230B VAL* 4.2 5.2 - - + -
231B GLY* 4.2 7.0 - - - +
234B VAL* 5.8 0.4 - - + -
260B HIS* 3.8 2.8 - - - -
261B LEU* 2.8 47.9 + - + +
263B VAL* 4.0 24.9 - - + -
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Residues in contact with LEU 205 (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 LEU* 4.5 8.1 - - + -
175B MET* 3.6 42.0 - - + -
188B VAL* 3.3 4.0 - - - -
189B VAL* 2.8 48.8 + - + +
191B ILE* 3.7 30.5 - - + -
203B LEU* 4.0 20.2 - - + +
204B VAL* 1.3 75.3 - - - +
206B PRO* 1.3 67.7 - - + +
260B HIS* 3.3 41.3 - - + +
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Residues in contact with PRO 206 (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 MET* 4.0 9.7 - - - +
187B GLN 3.3 10.3 - - - +
188B VAL* 4.1 2.5 - - + -
205B LEU* 1.3 87.1 - - + +
207B TRP* 1.3 63.6 + - - +
208B THR 3.6 21.4 - - - +
209B SER* 4.2 11.2 + - - -
210B ILE* 4.8 7.2 - - + +
223B LEU* 3.8 28.0 - - + -
227B MET* 4.0 16.8 - - + -
259B VAL 3.6 24.0 - - - +
260B HIS* 4.9 1.6 - - + -
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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