Contacts of the strand formed by residues 201 - 206 (chain B) in PDB entry 4JHN
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
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Residue Dist Surf HB Arom Phob DC
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171B GLN* 4.0 4.2 - - - +
198B GLY* 2.7 35.9 + - - +
199B TYR 3.7 0.4 - - - -
200B TYR* 1.3 82.2 + - - +
202B SER* 1.3 59.1 + - - +
213B VAL* 4.3 9.9 - - + -
214B PHE 3.5 14.4 - - - +
215B GLY* 4.2 0.9 - - - -
216B GLU 4.2 1.6 - - - +
221B LYS* 3.6 40.2 + - + +
222B LEU* 3.8 12.8 - - + -
250B CYS* 3.6 20.6 - - + +
251B GLY 3.5 25.2 + - - -
252B GLY 4.5 0.8 + - - -
254B HIS 3.5 13.9 + - - -
255B THR* 2.8 27.1 + - - -
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Residues in contact with SER 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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151B THR* 4.9 3.1 + - - -
163B MET* 3.8 13.7 - - - +
171B GLN* 2.7 27.7 + - - +
195B ILE* 5.4 0.2 - - - -
196B SER 3.3 13.7 - - - -
197B CYS* 3.7 12.5 - - - +
198B GLY 5.0 0.3 + - - -
201B HIS* 1.3 78.2 + - - +
203B ALA* 1.3 62.8 + - - +
213B VAL* 3.4 4.9 - - - +
214B PHE* 2.9 45.8 + - - +
250B CYS* 3.9 4.3 - - - -
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Residues in contact with ALA 203 (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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195B ILE* 3.4 7.5 - - - +
196B SER 2.9 30.9 + - - -
202B SER* 1.3 77.7 - - - +
204B PHE* 1.3 64.3 + - - +
211B LEU* 4.0 1.3 - - + -
212B TYR 3.1 13.5 - - - +
213B VAL* 3.9 13.9 - - + -
214B PHE* 4.1 2.9 - - - -
248B VAL* 3.8 22.8 - - + +
250B CYS* 3.7 16.4 - - - -
255B THR* 5.3 0.2 - - + -
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Residues in contact with PHE 204 (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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161B LEU* 3.7 23.3 - - + -
186B VAL* 4.2 9.9 - - + -
187B THR* 5.2 1.3 - - - -
188B ILE* 3.9 24.2 - - + -
190B LYS 5.8 0.2 - - - -
192B VAL* 3.8 28.3 - - + -
194B TRP 3.1 13.2 - - - +
195B ILE* 4.3 2.2 - - + +
203B ALA* 1.3 74.6 - - - +
205B VAL* 1.3 68.2 + - - +
206B THR* 4.1 6.3 - - + -
210B GLU 3.8 0.3 - - - +
211B LEU* 3.6 3.5 - - - +
212B TYR* 2.8 64.6 + + + +
214B PHE* 3.4 35.0 - + - -
235B PRO* 3.6 21.8 - - + -
248B VAL* 4.5 0.7 - - - -
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Residues in contact with VAL 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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192B VAL* 3.4 4.0 - - - +
193B SER* 2.7 38.1 + - - +
194B TRP* 2.8 26.4 + - + -
204B PHE* 1.3 79.0 - - - +
206B THR* 1.3 67.0 + - - +
209B GLY 4.4 1.1 - - - -
210B GLU 3.3 10.1 - - - +
211B LEU* 4.1 3.6 - - + -
245B VAL* 3.3 51.8 - - + +
246B ILE* 4.2 4.0 - - - +
247B GLN 4.2 1.3 - - - -
248B VAL* 3.8 24.2 - - + +
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Residues in contact with THR 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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188B ILE* 4.1 1.8 - - + -
190B LYS* 3.9 25.8 - - + +
191B PRO 3.4 10.8 - - - +
192B VAL* 4.2 0.7 - - + +
193B SER* 3.3 9.2 + - - -
204B PHE* 4.1 13.0 - - + -
205B VAL* 1.3 81.2 - - - +
207B THR* 1.3 60.1 + - - +
208B ASP* 2.5 28.2 + - - -
209B GLY* 2.9 17.5 + - - -
210B GLU* 2.8 22.4 + - - +
212B TYR* 3.7 28.7 - - + -
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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