Contacts of the helix formed by residues 191 - 205 (chain B) in PDB entry 1F5Q
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 ARG 191 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28B GLU* 2.9 39.4 + - - +
31B HIS* 3.5 26.5 + - + +
32B ASP* 3.7 21.8 + - - -
190B LYS* 1.3 77.0 - - - +
192B PRO* 1.3 74.7 - - + +
193B VAL* 4.5 4.5 - - + -
194B LEU* 3.4 17.4 + - + +
195B ILE* 3.3 18.2 + - - +
224B ILE* 6.3 3.4 - - - -
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Residues in contact with PRO 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B SER* 4.1 24.7 - - - +
28B GLU* 5.2 1.8 - - - +
31B HIS* 3.7 20.4 - - + +
34B ARG* 4.5 16.2 - - - +
147B CYS 4.5 8.1 - - - +
148B LEU* 5.5 0.2 - - - -
149B SER* 3.1 19.7 + - - +
152B LEU* 3.5 19.5 - - + -
190B LYS 4.0 1.8 - - - +
191B ARG* 1.3 84.0 - - + +
193B VAL* 1.3 59.8 + - - +
195B ILE* 3.2 4.2 + - + +
196B THR* 2.8 28.6 + - - -
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Residues in contact with VAL 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ILE* 3.7 36.6 - - + -
27B SER* 4.7 2.7 - - - +
28B GLU* 3.4 25.8 - - - +
152B LEU* 3.7 20.0 - - + -
156B ILE* 4.5 11.0 - - + -
191B ARG* 4.5 5.8 - - + -
192B PRO* 1.3 76.3 - - - +
194B LEU* 1.3 54.3 + - - +
196B THR* 3.0 4.1 + - - -
197B LEU* 2.5 48.4 + - + +
222B LEU* 4.5 11.7 - - + -
224B ILE* 4.7 11.0 - - + -
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Residues in contact with LEU 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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190B LYS* 4.0 24.9 - - + +
191B ARG* 3.4 22.2 + - + +
192B PRO 3.3 0.6 - - - -
193B VAL* 1.3 82.7 - - + +
195B ILE* 1.3 56.9 + - - +
197B LEU* 4.1 3.3 - - - +
198B ALA* 2.9 30.1 + - - +
224B ILE* 3.6 36.8 - - + -
228B GLU* 4.0 28.7 - - + +
229B LEU* 4.1 9.2 - - + -
232B CYS* 3.6 24.9 - - + -
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Residues in contact with ILE 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B SER* 3.8 21.1 - - - +
178B ILE* 4.4 7.4 - - + -
181B ALA* 4.3 22.4 - - + -
182B LEU* 5.5 7.9 - - + -
187B SER 3.1 28.3 - - - +
188B ALA* 4.5 7.4 - - - +
190B LYS* 3.5 27.8 - - + +
191B ARG 3.3 5.8 + - - +
192B PRO* 3.2 7.4 + - + +
193B VAL 3.2 0.4 - - - -
194B LEU* 1.3 74.4 - - - +
196B THR* 1.3 64.5 + - - +
198B ALA* 3.4 1.9 + - - +
199B CYS* 3.0 40.2 + - - -
232B CYS* 4.2 10.3 - - - -
236B VAL* 5.2 4.3 - - + -
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Residues in contact with THR 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B SER* 2.9 25.2 + - - -
152B LEU* 3.5 5.4 - - - +
153B ILE* 3.4 35.4 - - + +
156B ILE* 3.3 25.6 - - + -
174B CYS* 5.1 0.2 - - - -
178B ILE* 5.3 1.3 - - - -
192B PRO 2.8 17.4 + - - -
193B VAL* 3.2 12.1 - - - -
195B ILE* 1.3 77.6 - - - +
197B LEU* 1.3 56.9 + - - +
199B CYS* 3.2 6.5 + - - +
200B MET* 2.8 34.7 + - - +
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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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156B ILE* 3.9 34.5 - - + -
160B MET* 4.9 0.9 - - + -
193B VAL 2.5 20.4 + - - +
194B LEU 4.1 2.0 - - - +
196B THR* 1.3 73.8 - - - +
198B ALA* 1.3 52.9 + - - +
200B MET* 3.3 7.7 + - + +
201B HIS* 2.7 34.8 + - - +
211B TYR* 4.3 2.9 + - + -
215B ILE* 3.8 23.1 - - + -
218B VAL* 4.2 8.3 - - + -
219B CYS* 4.4 12.6 - - - -
222B LEU* 4.2 15.3 - - + -
224B ILE* 3.5 32.5 - - + -
229B LEU* 3.7 16.4 - - + +
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Residues in contact with ALA 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B LEU 2.9 21.0 + - - +
195B ILE* 3.5 5.6 - - - +
196B THR 3.2 0.2 - - - -
197B LEU* 1.3 76.3 - - - +
199B CYS* 1.3 63.0 + - - +
201B HIS* 3.1 4.2 + - - +
202B LEU* 3.0 28.7 + - - +
229B LEU* 3.7 10.0 - - + +
232B CYS* 3.8 27.1 - - + -
233B CYS* 3.8 14.9 - - - +
236B VAL* 4.2 7.6 - - + -
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Residues in contact with CYS 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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174B CYS* 3.9 20.9 - - + -
177B LYS* 3.6 24.9 - - + -
178B ILE* 3.6 28.9 - - + -
195B ILE* 3.0 29.3 + - - +
196B THR* 3.7 3.8 - - - +
198B ALA* 1.3 75.0 - - - +
200B MET* 1.3 63.2 + - - +
202B LEU* 3.3 11.2 + - - +
203B THR* 3.1 28.8 + - - +
236B VAL* 4.2 12.8 - - - -
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Residues in contact with MET 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B ILE* 3.5 23.6 - - + +
156B ILE* 3.5 37.0 - - + -
157B LEU* 3.4 33.2 - - + -
160B MET* 5.1 1.3 - - + -
170B ILE* 4.8 0.2 - - + -
174B CYS* 4.0 14.1 - - - -
196B THR* 2.8 32.5 + - + +
197B LEU* 3.5 9.2 - - + +
199B CYS* 1.3 77.2 - - - +
201B HIS* 1.3 52.5 + - - +
203B THR* 3.2 6.2 + - - -
204B MET* 2.6 57.9 + - + +
211B TYR* 4.2 7.2 - - + -
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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
----------------------------------------------------------
197B LEU 2.7 15.0 + - - +
198B ALA* 3.3 10.5 - - - +
200B MET* 1.3 74.0 - - - +
202B LEU* 1.3 60.1 + - - +
205B ASN* 2.8 59.3 + - + +
211B TYR* 2.7 34.6 + + - +
215B ILE* 5.3 1.5 - - + +
226B LYS* 6.5 0.2 - - - -
229B LEU* 3.8 15.3 - - + +
230B HIS* 4.0 16.9 + + - -
233B CYS* 3.8 21.3 - - - -
38C ASP* 2.7 31.1 + - + -
73C GLU 5.7 0.2 - - - +
74C ASN* 3.8 8.5 - - - +
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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
----------------------------------------------------------
177B LYS* 3.8 31.2 - - + -
198B ALA 3.0 19.5 + - - +
199B CYS* 3.4 9.6 - - - +
201B HIS* 1.3 77.7 - - - +
203B THR* 1.3 59.6 + - - +
207B LYS* 5.3 0.7 + - - -
233B CYS* 4.0 21.3 - - + +
236B VAL* 3.9 27.8 - - + -
237B ASP* 3.8 24.9 - - - +
73C GLU* 3.2 44.9 - - - +
74C ASN* 4.0 21.1 - - - +
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Residues in contact with THR 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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170B ILE* 4.7 4.2 - - - +
173B LEU* 3.9 41.8 - - + +
174B CYS* 3.7 9.6 - - - -
177B LYS* 3.7 23.3 - - + -
199B CYS 3.1 18.0 + - - +
200B MET* 3.2 8.7 + - - -
201B HIS 3.0 0.2 - - - -
202B LEU* 1.3 82.1 - - - +
204B MET* 1.3 68.0 + - - +
205B ASN 3.7 0.7 - - - -
207B LYS* 3.7 21.9 - - - +
208B TYR* 3.8 8.1 - - - -
73C GLU* 4.5 2.7 - - - +
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Residues in contact with MET 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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157B LEU* 3.5 25.6 - - + -
160B MET* 4.5 2.9 - - - -
170B ILE* 4.1 17.7 - - + -
200B MET* 2.6 50.2 + - + +
203B THR* 1.3 80.6 - - - +
205B ASN* 1.3 65.5 + - - +
206B GLN 3.2 1.0 + - - -
207B LYS* 3.0 14.5 + - - -
208B TYR* 3.3 26.1 + - + +
210B TYR* 3.6 25.8 - - + +
211B TYR* 3.6 36.0 - - + -
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Residues in contact with ASN 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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200B MET 3.9 0.2 + - - -
201B HIS* 2.8 56.2 + - + +
203B THR 3.7 0.7 - - - -
204B MET* 1.3 76.5 - - - +
206B GLN* 1.3 100.1 + - - +
207B LYS* 3.3 14.7 + - - +
211B TYR* 3.7 13.7 - - - -
212B GLU* 6.2 1.4 - - - +
38C ASP* 4.1 7.7 - - - +
73C GLU 4.2 5.0 - - - +
74C ASN* 3.9 19.2 - - + +
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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
------------------------------------------------------------
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