Contacts of the helix formed by residues 201 - 213 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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199D ILE 3.3 1.2 + - - -
200D GLY* 1.3 69.2 - - - -
202D SER* 1.3 56.5 + - - +
203D LYS* 3.3 2.9 - - - +
204D ARG* 3.4 16.8 + - + +
205D LEU* 2.9 28.7 + - - +
372D THR* 4.5 11.6 + - + +
208F ASP* 4.3 13.9 - - + +
211F ALA* 4.8 5.2 - - + -
212F GLU* 4.3 20.8 - - - +
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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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192D GLY 2.6 27.1 + - - -
194D PHE* 3.8 18.2 - - - -
198D GLY* 3.5 2.3 - - - -
199D ILE* 3.0 32.5 + - - -
200D GLY 3.2 2.0 + - - -
201D ALA* 1.3 73.3 - - - +
203D LYS* 1.3 61.3 + - - +
205D LEU* 4.1 6.5 - - - -
206D VAL* 2.9 37.1 + - - +
358D PHE* 3.9 12.6 - - - -
372D THR* 4.7 1.3 - - - +
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Residues in contact with LYS 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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190D TYR* 3.4 53.1 - - + +
191D LEU 3.2 18.6 - - - +
200D GLY 4.9 0.6 + - - -
201D ALA* 4.4 0.6 - - - +
202D SER* 1.3 81.1 + - - +
204D ARG* 1.3 73.0 + - + +
206D VAL* 4.1 0.3 - - - +
207D GLU* 3.1 55.3 + - - +
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Residues in contact with ARG 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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204B ARG* 3.1 44.6 - - - +
201D ALA* 3.4 17.3 + - + +
202D SER 3.4 0.4 - - - -
203D LYS* 1.3 88.3 - - + +
205D LEU* 1.3 62.2 + - - +
207D GLU* 3.6 2.2 + - - +
208D ASP* 3.1 33.0 + - - +
204F ARG* 3.4 34.2 + - - +
207F GLU* 3.4 24.5 + - - +
208F ASP* 2.5 50.0 + - - +
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Residues in contact with LEU 205 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201D ALA 2.9 18.3 + - - +
202D SER* 3.6 5.2 - - - +
204D ARG* 1.3 77.9 - - - +
206D VAL* 1.3 66.6 + - + +
208D ASP* 3.5 5.7 + - - +
209D LEU* 3.0 48.8 + - + +
351D PHE* 5.2 3.8 - - + -
356D GLY* 5.6 0.4 - - - -
358D PHE* 3.9 24.0 - - + -
372D THR* 3.5 26.9 - - + -
373D LYS 4.5 6.5 - - - +
374D MET* 4.4 24.5 - - + -
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Residues in contact with VAL 206 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161D TYR* 3.4 35.0 - - + -
165D LEU* 5.8 0.4 - - + -
191D LEU* 4.3 8.7 - - + -
192D GLY* 4.0 19.5 - - - +
194D PHE* 4.2 13.7 - - + -
202D SER 2.9 18.2 + - - +
203D LYS 4.3 1.8 - - - +
205D LEU* 1.3 86.5 - - + +
207D GLU* 1.3 61.9 + - - +
209D LEU* 3.3 11.0 + - + +
210D PHE* 2.8 39.6 + - + +
351D PHE* 6.5 0.4 - - + -
358D PHE* 4.8 2.2 - - + -
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Residues in contact with GLU 207 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B ARG* 3.0 28.8 + - - +
190D TYR* 5.3 0.7 - - - +
191D LEU* 4.0 27.8 + - + +
203D LYS* 3.1 52.4 + - - +
204D ARG* 3.9 1.3 - - - +
206D VAL* 1.3 78.0 - - - +
208D ASP* 1.3 56.1 + - - +
210D PHE* 3.4 2.5 + - - +
211D ALA* 2.9 30.8 + - - +
217D TRP* 3.9 30.1 + - + +
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Residues in contact with ASP 208 (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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201B ALA* 3.9 18.2 - - + +
204B ARG* 2.8 38.6 + - - -
204D ARG* 3.1 20.5 + - - +
205D LEU* 3.7 6.1 - - - +
207D GLU* 1.3 72.1 - - - +
209D LEU* 1.3 61.4 + - + +
211D ALA* 3.3 5.4 + - - +
212D GLU* 2.9 47.3 + - - +
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Residues in contact with LEU 209 (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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165D LEU* 4.4 10.1 - - + -
205D LEU* 3.0 29.6 + - + +
206D VAL* 3.3 15.5 - - + +
208D ASP* 1.3 76.1 - - + +
210D PHE* 1.3 66.9 + - + +
212D GLU* 3.4 11.6 + - - +
213D ARG* 3.1 59.6 + - - +
351D PHE* 3.5 37.7 - - + -
374D MET* 3.6 26.9 - - + -
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Residues in contact with PHE 210 (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 TYR* 3.6 25.6 - + - -
164D ALA* 4.7 4.3 - - + -
165D LEU* 3.6 33.4 - - + -
184D PHE* 3.5 42.8 - + + -
191D LEU* 3.6 23.1 - - + -
206D VAL* 2.8 24.0 + - + +
207D GLU 3.8 3.8 - - - +
209D LEU* 1.3 76.3 - - + +
211D ALA* 1.3 57.0 + - - +
213D ARG 3.5 0.2 - - - -
214D ASN* 2.9 8.8 + - - -
215D ILE* 2.8 61.4 + - + +
217D TRP* 3.9 18.4 - + + +
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Residues in contact with ALA 211 (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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200B GLY* 3.4 39.5 + - - +
201B ALA* 4.2 3.6 - - + +
367B ARG* 5.7 1.9 + - - -
370B VAL* 4.1 3.6 - - - +
207D GLU 2.9 18.1 + - - +
208D ASP* 3.7 6.3 - - - +
210D PHE* 1.3 74.8 - - - +
212D GLU* 1.3 64.2 + - - +
213D ARG 3.3 0.7 + - - -
214D ASN* 3.4 11.2 + - - +
217D TRP* 5.6 1.9 - - - +
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Residues in contact with GLU 212 (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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200B GLY* 4.3 9.2 - - - -
201B ALA* 5.0 7.2 - - + +
369B ARG* 5.1 2.3 - - - -
370B VAL* 3.3 32.6 + - + +
372B THR* 5.5 5.0 + - - +
208D ASP* 2.9 36.9 + - - +
209D LEU* 3.9 16.7 - - - +
211D ALA* 1.3 72.1 - - - +
213D ARG* 1.3 67.8 + - + +
214D ASN* 3.5 0.6 - - - +
374D MET* 5.9 0.5 - - - +
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Residues in contact with ARG 213 (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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367B ARG 5.5 0.7 - - - -
165D LEU* 3.9 19.0 - - + +
168D HIS* 3.3 42.1 + - + +
177D ARG* 2.8 31.5 + - - -
209D LEU* 3.1 50.9 + - - +
212D GLU* 1.3 86.3 + - + +
214D ASN* 1.3 57.9 + - - +
215D ILE* 3.3 11.5 + - + +
351D PHE* 4.3 8.6 - - - -
354D ASP* 3.1 31.2 + - - -
374D MET* 3.6 10.7 - - - +
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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