Contacts of the helix formed by residues 192 - 204 (chain B) in PDB entry 4HYJ
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 192 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154B TRP* 3.5 26.2 - - + -
188B LEU 3.6 13.9 + - - +
189B ILE* 3.2 15.2 + - + +
191B TRP* 1.3 76.7 - - - +
193B ILE* 1.3 63.4 + - - +
195B PRO* 3.1 16.0 - - - +
196B ILE* 3.3 25.6 + - + +
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Residues in contact with ILE 193 (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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189B ILE 4.0 6.3 + - - +
190B GLY 3.7 18.2 - - - +
191B TRP 3.1 0.8 + - - -
192B ALA* 1.3 77.7 - - + +
194B TYR* 1.3 57.2 + - + +
196B ILE* 3.3 11.2 + - + +
197B GLY 3.0 23.7 + - - -
216B ILE* 3.7 31.0 - - + -
217B TYR* 3.7 12.8 - - + -
220B ALA* 3.9 28.0 - - + +
311B LFA 4.1 25.1 - - + -
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Residues in contact with TYR 194 (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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86B TRP* 3.5 25.1 - + + -
190B GLY 4.0 4.9 - - - -
191B TRP* 3.2 15.0 + - - -
193B ILE* 1.3 75.8 - - - +
195B PRO* 1.4 68.8 - - + +
196B ILE 3.2 0.2 + - - -
197B GLY 3.2 0.5 + - - -
198B TYR* 3.0 8.7 + - - +
217B TYR* 2.4 48.5 + + + +
220B ALA* 3.3 13.1 - - + -
221B ASP* 2.6 39.3 + - - -
224B ASN* 3.0 32.7 + - - -
301B RET 3.3 58.0 - - + +
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Residues in contact with PRO 195 (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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147B TYR* 2.6 42.3 + - + +
151B CYS* 4.4 5.4 - - - -
154B TRP* 4.1 17.9 - - + -
191B TRP 3.2 12.1 - - - +
192B ALA 3.1 17.9 - - - +
194B TYR* 1.4 93.6 - - + +
196B ILE* 1.3 55.4 + - + -
198B TYR* 3.3 3.8 - - + +
199B ALA* 2.9 17.3 + - - +
301B RET 3.8 36.1 - - + -
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Residues in contact with ILE 196 (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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147B TYR* 4.7 0.7 - - - -
192B ALA* 3.3 28.4 + - + +
193B ILE* 3.6 12.8 - - + +
194B TYR 3.1 1.2 - - - -
195B PRO* 1.3 76.4 - - + +
197B GLY* 1.3 65.3 + - - +
199B ALA* 3.0 8.3 + - - +
200B VAL* 3.0 33.7 + - + +
319B LFA 5.2 11.4 - - + -
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Residues in contact with GLY 197 (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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193B ILE 3.0 12.9 + - - -
194B TYR 3.2 0.2 + - - -
196B ILE* 1.3 77.1 - - - +
198B TYR* 1.3 58.8 + - - +
200B VAL* 4.1 8.0 - - - +
201B THR* 2.8 28.9 + - - -
213B ARG* 3.1 11.8 + - - +
217B TYR* 3.5 20.9 - - - -
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Residues in contact with TYR 198 (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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126B GLY* 3.8 10.3 - - - -
129B GLY* 3.1 23.7 - - - -
130B GLU* 3.4 36.6 - - + -
133B ILE* 3.8 8.4 - - + +
143B GLY* 2.7 27.9 + - - -
147B TYR* 3.2 34.6 - + + +
194B TYR 3.0 12.6 + - - +
195B PRO* 3.3 11.4 - - + +
197B GLY* 1.3 75.4 - - - +
199B ALA* 1.3 55.4 + - - +
201B THR* 3.1 5.2 + - + -
202B LEU* 2.7 49.3 + - + -
213B ARG* 3.5 11.4 - - - +
301B RET 3.7 22.0 - - + -
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Residues in contact with ALA 199 (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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147B TYR* 3.7 15.7 - - + +
195B PRO 2.9 14.4 + - - +
196B ILE* 3.0 8.0 + - - +
198B TYR* 1.3 79.1 - - - +
200B VAL* 1.3 63.5 + - - +
202B LEU* 3.1 19.6 + - + +
203B PHE* 3.1 18.2 + - + +
305B LFA 5.8 6.1 - - + -
319B LFA 4.0 28.7 - - + -
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Residues in contact with VAL 200 (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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196B ILE* 3.0 27.0 + - + +
197B GLY* 4.2 7.0 - - - +
199B ALA* 1.3 74.1 - - + +
201B THR* 1.3 56.4 + - - +
203B PHE* 3.1 1.9 + - - +
204B ALA* 2.8 43.8 + - + +
209B ILE* 3.7 24.7 - - + -
319B LFA 5.3 11.0 - - + -
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Residues in contact with THR 201 (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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130B GLU* 5.4 1.6 - - + +
133B ILE* 5.2 19.6 - - + +
197B GLY 2.8 21.1 + - - -
198B TYR* 3.1 6.7 + - + +
200B VAL* 1.3 80.1 - - - +
202B LEU* 1.3 64.2 + - - +
203B PHE 3.5 0.3 + - - -
204B ALA 4.1 6.4 + - - -
205B PRO* 4.2 15.0 - - + +
209B ILE* 5.1 4.9 - - - +
210B GLN* 4.6 21.5 - - + +
213B ARG* 3.1 39.8 - - - +
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Residues in contact with LEU 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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133B ILE* 3.6 30.6 - - + +
138B GLY 5.4 0.2 - - - -
139B PHE* 3.7 50.0 + - + +
140B THR 4.7 0.9 - - - +
143B GLY 4.0 14.6 - - - +
144B LEU* 4.2 24.5 - - + -
147B TYR* 4.8 5.2 - - + -
198B TYR* 2.7 38.7 + - + +
199B ALA* 3.1 13.2 + - - +
201B THR* 1.3 76.2 - - - +
203B PHE* 1.3 68.9 + - + +
204B ALA 3.6 0.4 + - - -
205B PRO* 4.8 5.2 - - - +
305B LFA 5.4 3.8 - - + -
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Residues in contact with PHE 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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139B PHE* 5.2 1.8 - + - -
199B ALA* 3.1 13.9 + - + +
200B VAL* 3.1 4.7 + - - +
202B LEU* 1.3 90.9 - - + +
204B ALA* 1.3 61.2 + - - +
205B PRO* 3.9 5.2 - - - +
305B LFA 4.5 23.1 - - + -
319B LFA 4.0 40.9 - - + +
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Residues in contact with ALA 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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200B VAL* 2.8 26.1 + - + +
201B THR* 4.9 0.3 - - - -
202B LEU 3.6 0.2 - - - -
203B PHE* 1.3 81.8 - - - +
205B PRO* 1.3 71.8 - - - +
209B ILE* 3.4 27.9 - - + +
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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