Contacts of the helix formed by residues 201 - 213 (chain B) in PDB entry 3HYW
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 ALA 201 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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199B ILE 3.3 0.8 + - - -
200B GLY* 1.3 69.3 - - - -
202B SER* 1.3 56.8 + - - +
203B LYS* 3.3 4.0 + - - +
204B ARG* 3.4 12.9 + - + +
205B LEU* 3.0 27.9 + - - +
372B THR* 4.2 13.9 + - - +
208D ASP* 3.9 33.2 - - + +
211D ALA* 4.2 3.8 - - + +
212D GLU* 5.0 7.9 - - + +
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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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192B GLY 2.6 28.8 + - - -
194B PHE* 3.8 8.3 - - - -
198B GLY* 3.4 2.6 - - - -
199B ILE 2.9 33.4 + - - -
200B GLY 3.2 2.1 + - - -
201B ALA* 1.3 75.8 - - - +
203B LYS* 1.3 56.7 + - - +
205B LEU* 3.7 6.2 - - - +
206B VAL* 2.9 35.4 + - - +
358B PHE* 3.7 22.0 - - - -
372B THR* 4.9 0.4 - - - -
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Residues in contact with LYS 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B TYR* 3.7 38.7 - - + +
191B LEU 3.1 24.7 - - - +
200B GLY 5.0 0.4 + - - -
201B ALA* 3.3 1.3 - - - -
202B SER* 1.3 77.7 + - - +
204B ARG* 1.3 60.1 + - - +
206B VAL* 4.0 0.2 - - - -
207B GLU* 3.0 63.3 + - - +
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Residues in contact with ARG 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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201B ALA* 3.4 15.0 + - + +
203B LYS* 1.3 78.2 - - - +
205B LEU* 1.3 63.6 + - - +
207B GLU* 3.7 2.5 - - - +
208B ASP* 3.0 33.1 + - - +
204D ARG* 3.1 44.9 + - - +
207D GLU* 3.0 34.8 + - - +
208D ASP* 2.8 37.2 + - - -
204F ARG* 3.1 44.7 - - - +
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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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201B ALA 3.0 16.8 + - - +
202B SER* 3.7 6.3 - - - +
204B ARG* 1.3 78.0 - - - +
206B VAL* 1.3 62.6 + - + +
208B ASP* 3.4 4.8 + - - +
209B LEU* 3.0 44.3 + - + +
351B PHE* 5.2 3.1 - - + -
356B GLY* 5.4 0.9 - - - -
358B PHE* 4.3 27.1 - - + -
372B THR* 4.6 14.4 - - - +
373B LYS 4.2 21.5 - - - +
374B MET* 4.5 24.2 - - + +
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Residues in contact with VAL 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B TYR* 3.5 34.8 - - + -
165B LEU* 6.0 0.7 - - + -
191B LEU* 3.9 18.2 - - + -
192B GLY* 4.2 3.1 - - - +
194B PHE* 4.2 23.3 - - + -
202B SER 2.9 24.3 + - - +
203B LYS 4.3 1.6 - - - +
205B LEU* 1.3 80.7 - - + +
207B GLU* 1.3 60.6 + - - +
209B LEU* 3.2 10.7 + - + +
210B PHE* 2.8 40.9 + - + +
351B PHE* 6.1 2.2 - - + -
358B PHE* 4.7 4.3 - - + -
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Residues in contact with GLU 207 (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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190B TYR* 5.2 0.7 - - - +
191B LEU* 3.8 27.1 + - + +
203B LYS* 3.0 52.8 + - - +
204B ARG* 3.7 1.3 - - - +
206B VAL* 1.3 77.0 - - - +
208B ASP* 1.3 56.7 + - - +
210B PHE* 3.7 2.4 - - - +
211B ALA* 2.9 29.7 + - - +
217B TRP* 4.0 29.7 + - + +
204F ARG* 2.9 28.2 + - - +
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Residues in contact with ASP 208 (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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204B ARG* 3.0 21.4 + - - +
205B LEU* 3.7 6.0 - - - +
207B GLU* 1.3 72.7 - - - +
209B LEU* 1.3 60.9 + - - +
211B ALA* 3.3 6.2 + - - +
212B GLU* 2.8 49.4 + - - +
201F ALA* 4.0 15.5 - - + +
204F ARG* 2.6 41.0 + - - -
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Residues in contact with LEU 209 (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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165B LEU* 3.7 24.0 - - + -
205B LEU* 3.0 27.6 + - + +
206B VAL* 3.2 11.0 + - + +
208B ASP* 1.3 76.7 - - - +
210B PHE* 1.3 62.9 + - + +
212B GLU* 3.5 11.1 + - - +
213B ARG* 3.1 67.3 + - - +
351B PHE* 3.3 37.2 - - + -
374B MET* 4.0 18.4 - - + -
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Residues in contact with PHE 210 (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 TYR* 3.5 24.0 - + - -
164B ALA* 4.9 3.1 - - + -
165B LEU* 3.9 26.9 - - + -
184B PHE* 3.6 41.1 - + + -
191B LEU* 3.6 24.0 - - + -
206B VAL* 2.8 27.8 + - + +
207B GLU 3.7 4.0 - - - +
209B LEU* 1.3 72.7 - - + +
211B ALA* 1.3 60.4 + - - +
213B ARG 3.3 0.7 + - - -
214B ASN 3.0 9.5 + - - -
215B ILE* 2.8 68.1 + - + +
217B TRP* 3.9 16.8 - + + -
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Residues in contact with ALA 211 (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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207B GLU 2.9 18.1 + - - +
208B ASP* 3.3 5.8 + - - +
210B PHE* 1.3 75.7 - - - +
212B GLU* 1.3 62.8 + - - +
213B ARG 3.3 0.9 + - - -
214B ASN* 3.3 12.1 + - - +
215B ILE 5.2 1.1 - - - -
217B TRP* 5.6 1.7 - - - +
200F GLY* 3.4 36.8 + - - +
201F ALA* 4.0 9.6 - - + +
370F VAL* 4.6 1.0 - - - +
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Residues in contact with GLU 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B ASP* 2.8 37.5 + - - +
209B LEU* 3.8 19.5 - - - +
211B ALA* 1.3 73.5 - - - +
213B ARG* 1.3 68.6 + - + +
214B ASN 3.8 0.2 + - - -
374B MET* 5.6 4.7 - - - +
200F GLY* 4.1 8.3 - - - -
201F ALA* 4.7 15.6 - - + +
369F ARG* 5.9 0.5 - - - -
370F VAL* 3.3 24.2 + - + +
372F THR* 5.5 4.5 - - - +
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Residues in contact with ARG 213 (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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165B LEU* 3.7 20.4 + - - +
168B HIS* 3.2 39.0 + - + +
172B LYS* 6.1 0.7 - - - +
177B ARG* 2.9 29.8 + - - -
209B LEU* 3.1 41.4 + - - +
210B PHE 4.4 0.9 - - - +
211B ALA 3.2 0.2 - - - -
212B GLU* 1.3 88.0 + - + +
214B ASN* 1.3 55.6 + - - +
215B ILE* 3.3 11.8 + - + +
351B PHE* 4.0 16.0 + - - +
354B ASP* 3.0 39.2 + - - -
374B MET* 4.9 5.9 - - - +
367F ARG 5.7 0.4 - - - -
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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