Contacts of the strand formed by residues 201 - 206 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171D GLN* 4.0 4.9 - - - +
198D GLY* 2.7 35.0 + - - +
199D TYR 3.7 0.4 - - - -
200D TYR* 1.3 82.7 + - - +
202D SER* 1.3 60.9 + - - +
213D VAL* 5.8 3.1 - - + -
214D PHE 3.5 13.5 - - - +
215D GLY* 4.1 0.9 - - - -
216D GLU 4.2 1.8 - - - +
221D LYS* 3.6 39.9 + - + +
222D LEU* 3.7 18.2 - - + -
250D CYS* 3.6 21.8 - - + +
251D GLY 3.5 20.2 + - - -
252D GLY 4.6 0.2 + - - -
254D HIS 3.5 18.7 + - - -
255D THR* 2.8 27.6 + - + -
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Residues in contact with SER 202 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151D THR* 4.9 2.9 + - - -
163D MET* 3.9 14.9 - - - +
171D GLN* 2.7 27.7 + - - +
172D ILE* 5.1 0.2 - - - +
196D SER 3.3 13.2 - - - -
197D CYS* 3.6 13.6 - - - +
198D GLY 4.9 0.5 + - - -
201D HIS* 1.3 79.2 + - - +
203D ALA* 1.3 64.7 + - - +
213D VAL* 3.6 2.3 - - - +
214D PHE* 2.9 45.9 + - - +
250D CYS* 4.0 4.9 - - - -
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Residues in contact with ALA 203 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195D ILE* 3.0 8.2 - - - +
196D SER 2.9 32.1 + - - -
202D SER* 1.3 77.8 - - - +
204D PHE* 1.3 60.8 + - - +
211D LEU* 4.3 2.7 - - + -
212D TYR 3.1 13.5 - - - +
213D VAL* 3.9 14.4 - - + -
214D PHE* 4.2 2.0 - - - -
248D VAL* 3.8 21.8 - - + +
250D CYS* 3.7 17.9 - - - -
255D THR* 5.4 0.2 - - + -
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Residues in contact with PHE 204 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161D LEU* 3.6 17.9 - - + -
186D VAL* 4.1 12.6 - - + -
187D THR* 5.1 1.3 - - - -
188D ILE* 3.9 27.6 - - + -
192D VAL* 3.8 24.2 - - + -
194D TRP 3.1 15.0 - - - +
195D ILE* 3.6 9.2 - - + -
203D ALA* 1.3 73.9 - - - +
205D VAL* 1.3 70.0 + - - +
206D THR* 4.1 6.5 - - + -
210D GLU 3.8 0.2 - - - +
211D LEU* 3.6 3.5 - - - +
212D TYR* 2.9 64.2 + + + +
214D PHE* 3.5 33.2 - + - -
235D PRO* 3.8 16.2 - - + -
248D VAL* 4.5 1.8 - - - -
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Residues in contact with VAL 205 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192D VAL* 3.4 4.3 - - - +
193D SER* 2.7 41.2 + - - +
194D TRP* 2.8 22.6 + - + -
204D PHE* 1.3 79.6 - - - +
206D THR* 1.3 67.5 + - - +
209D GLY* 4.2 1.1 - - - -
210D GLU 3.3 9.4 - - - +
211D LEU* 5.1 2.2 - - + -
245D VAL* 3.3 51.6 - - + +
246D ILE* 4.3 4.7 - - - +
248D VAL* 3.8 23.8 - - + +
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Residues in contact with THR 206 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188D ILE* 4.1 5.8 - - + -
190D LYS* 3.9 26.2 - - + +
191D PRO 3.3 11.0 - - - +
192D VAL* 4.2 0.7 - - + +
193D SER* 3.2 9.1 + - - -
204D PHE* 4.1 8.7 - - + -
205D VAL* 1.3 80.3 - - - +
207D THR* 1.3 60.4 + - - +
208D ASP* 2.4 28.2 + - - -
209D GLY* 2.9 17.3 + - - -
210D GLU* 2.9 20.8 + - - +
212D TYR* 3.8 29.2 - - + -
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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