Contacts of the helix formed by residues 195 - 207 (chain B) in PDB entry 4JA1
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 LEU 195 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108B LEU* 4.0 20.0 - - + -
113B VAL* 4.0 24.5 - - + +
116B ALA* 3.9 22.9 - - + -
117B VAL* 5.1 5.4 - - + -
146B PHE* 4.1 22.7 - - + -
180B PHE* 3.9 24.2 - - + -
186B TRP* 3.7 26.7 - - + -
187B THR 3.2 16.0 + - - +
188B LYS* 6.0 0.2 - - - -
193B THR 3.4 1.2 + - - -
194B ASN* 1.3 72.5 - - - +
196B PHE* 1.3 54.0 + - - +
198B VAL 3.8 0.3 - - - -
199B ALA* 2.8 40.4 + - + +
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Residues in contact with PHE 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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116B ALA* 3.8 22.7 - - + +
119B LYS* 3.6 41.5 - - + -
120B ALA* 3.6 19.3 - - - -
123B VAL* 3.7 11.7 - - + -
188B LYS 5.9 0.4 - - - +
194B ASN* 3.3 8.2 + - - +
195B LEU* 1.3 75.6 - - - +
197B LEU* 1.3 77.9 + - + +
199B ALA* 3.1 1.6 + - - +
200B ALA* 2.7 38.0 + - + +
229B LEU* 3.8 23.6 - - + -
232B PHE* 3.6 37.2 - + + -
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Residues in contact with LEU 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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194B ASN* 2.8 35.2 + - + +
196B PHE* 1.3 83.7 - - + +
198B VAL* 1.3 62.5 + - - +
200B ALA* 3.4 1.3 + - - -
201B HIS* 3.2 17.3 + - - +
218B LEU* 3.6 19.3 - - + +
223B TYR* 4.3 13.0 - - + +
224B HIS* 4.3 7.4 - - + +
227B THR* 2.9 38.6 - - + +
229B LEU* 4.0 9.0 - - + -
232B PHE* 3.7 36.6 - - + -
306B NGH 4.2 4.2 - - - +
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Residues in contact with VAL 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B LEU* 4.1 8.1 - - + -
165B ALA* 3.8 29.2 - - + -
180B PHE* 3.8 4.7 - - + -
186B TRP* 3.8 16.6 - - + -
193B THR* 3.8 16.8 - - + -
194B ASN 3.2 17.4 + - - +
197B LEU* 1.3 74.6 - - - +
199B ALA* 1.3 61.6 + - - +
201B HIS* 3.3 2.4 + - - +
202B GLU* 2.9 26.3 + - - +
223B TYR* 3.8 25.4 - - + -
306B NGH 3.8 23.1 - - + +
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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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116B ALA 4.7 3.1 - - - +
117B VAL* 5.0 10.5 - - + -
120B ALA* 3.7 16.2 - - + -
180B PHE* 3.7 24.8 - - + -
195B LEU* 2.8 28.6 + - + +
196B PHE* 3.7 3.8 - - - +
198B VAL* 1.3 73.3 - - - +
200B ALA* 1.3 59.0 + - - +
202B GLU* 3.3 0.7 + - - +
203B ILE* 2.8 37.9 + - + +
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Residues in contact with ALA 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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120B ALA* 3.5 22.3 - - + +
123B VAL* 4.5 9.0 - - + -
124B TRP* 2.9 28.2 + - - +
196B PHE* 2.7 30.4 + - + +
197B LEU* 3.7 4.7 - - - +
199B ALA* 1.3 73.3 - - - +
201B HIS* 1.3 56.4 + - - +
204B GLY 3.0 11.4 + - - -
218B LEU* 3.7 21.5 - - + -
232B PHE* 5.2 1.1 - - + -
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Residues in contact with HIS 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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197B LEU 3.2 5.2 + - - +
198B VAL 3.6 4.3 - - - +
200B ALA* 1.3 77.1 - - - +
202B GLU* 1.3 69.6 + - - +
204B GLY 3.1 8.8 + - - -
205B HIS* 3.1 11.0 + - - -
211B HIS* 3.8 5.4 - + - -
218B LEU* 2.8 26.4 + - + +
219B MET* 3.3 47.4 - - + +
220B TYR 3.8 9.4 - - - -
221B PRO* 4.0 4.7 - - + -
301B ZN 2.1 36.2 - - - -
306B NGH 3.0 45.0 + + - +
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Residues in contact with GLU 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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165B ALA* 3.6 25.6 - - + +
166B HIS* 3.0 28.1 - - - +
167B ALA* 3.1 12.1 + - + +
178B ALA* 4.2 11.9 - - + -
180B PHE* 4.1 11.2 - - + -
198B VAL* 2.9 22.5 + - + +
199B ALA 3.8 3.8 - - - +
201B HIS* 1.3 74.1 - - - +
203B ILE* 1.3 58.8 + - - +
205B HIS* 2.9 22.4 + - - +
206B SER* 2.9 16.9 + - - -
306B NGH 2.6 47.0 + - - -
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Residues in contact with ILE 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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117B VAL* 6.1 0.9 - - + -
120B ALA* 4.6 8.5 - - + +
121B LEU* 3.9 34.8 - - + -
124B TRP* 3.4 24.2 - - + +
132B PHE* 4.7 2.7 - - + -
142B ILE* 3.9 27.4 - - + -
144B ILE* 4.4 13.2 - - + -
178B ALA* 5.0 4.5 - - + -
180B PHE* 6.3 1.6 - - + -
199B ALA* 2.8 28.1 + - + +
200B ALA* 3.8 4.7 - - - +
202B GLU* 1.3 68.7 - - + +
204B GLY* 1.3 66.9 + - - +
206B SER* 2.9 18.8 + - - +
207B LEU* 2.9 34.5 + - + +
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Residues in contact with GLY 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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124B TRP* 3.6 28.8 - - - +
200B ALA 3.0 11.1 + - - -
201B HIS 3.1 6.9 + - - -
203B ILE* 1.3 77.7 - - - +
205B HIS* 1.3 58.5 + - - +
207B LEU* 3.5 6.5 + - - +
208B GLY 3.3 4.3 + - - -
209B LEU* 2.9 31.9 + - - +
219B MET* 3.8 7.6 - - - -
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Residues in contact with HIS 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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167B ALA* 3.8 20.9 - - + +
168B TYR 4.1 2.0 - - - -
169B ALA* 3.7 13.4 - - - +
201B HIS* 3.1 12.6 + + - -
202B GLU* 2.9 19.9 + - - +
204B GLY* 1.3 72.7 - - - +
206B SER* 1.3 56.1 + - - +
207B LEU 3.0 4.9 - - - -
208B GLY* 3.0 20.3 + - - -
209B LEU 2.7 23.8 + - - +
210B PHE* 4.0 18.8 - + - -
211B HIS* 3.3 14.8 + + - -
219B MET* 3.4 17.3 - - + +
301B ZN 2.1 37.3 - - - -
306B NGH 3.4 9.4 - - - -
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Residues in contact with SER 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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92B TRP* 2.7 31.6 + - - -
142B ILE* 4.3 15.7 - - - -
167B ALA* 3.9 8.1 - - - +
168B TYR 3.3 12.5 + - - -
170B PRO* 3.3 10.3 - - - +
176B GLY* 3.1 26.7 + - - -
177B ASP 4.1 0.7 + - - -
178B ALA* 4.3 2.4 - - - +
202B GLU 2.9 17.0 + - - -
203B ILE* 2.9 19.1 + - - +
205B HIS* 1.3 72.2 - - - +
207B LEU* 1.3 51.4 + - - +
208B GLY 3.5 0.2 - - - -
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Residues in contact with LEU 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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90B PRO 4.6 0.3 - - - +
92B TRP* 3.9 7.6 - - + +
97B LEU* 3.7 29.6 - - + -
124B TRP* 3.7 37.9 - - + -
130B LEU* 3.8 19.5 - - + -
132B PHE* 3.9 13.7 - - + -
142B ILE* 4.6 4.9 - - + -
170B PRO* 3.5 7.6 - - - +
203B ILE* 2.9 23.1 + - + +
204B GLY 3.8 4.9 - - - +
205B HIS 3.0 0.2 - - - -
206B SER* 1.3 79.2 - - - +
208B GLY* 1.4 55.5 + - - +
209B LEU 3.7 0.4 - - - -
242B ILE* 3.9 18.2 - - + -
245B LEU* 3.7 4.1 - - - +
246B TYR* 2.6 31.9 + - + -
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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