Contacts of the helix formed by residues 197 - 211 (chain B) in PDB entry 1H3F
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 GLN 197 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155B ARG* 5.0 8.3 - - - +
179B GLN* 3.3 13.3 + - - +
193B GLY* 4.4 4.9 - - - -
194B GLY 2.8 25.1 + - - +
196B ASP* 1.3 95.2 + - - +
198B ARG* 1.3 64.3 + - - +
199B PHE 3.4 2.2 - - - -
200B ASN* 3.3 15.1 + - - +
201B LEU* 3.1 33.6 + - + +
220B LEU* 4.6 1.1 - - - -
1433B TYE 2.4 42.5 + - - -
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Residues in contact with ARG 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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21B GLU* 2.7 45.1 + - - -
23B VAL* 3.8 22.0 - - - +
194B GLY 4.0 2.0 + - - -
195B THR 3.5 14.9 + - - +
196B ASP 3.4 2.2 - - - -
197B GLN* 1.3 78.5 - - - +
199B PHE* 1.3 64.5 + - - +
201B LEU* 3.3 2.8 + - - +
202B LEU* 3.1 46.9 + - + +
218B CYS* 5.7 1.0 - - - +
220B LEU* 3.7 21.6 - - + +
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Residues in contact with PHE 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B MET* 4.0 19.3 - - + -
151B GLN 3.8 18.4 - - - -
152B MET* 3.9 24.5 - - + -
154B GLU* 4.4 5.2 - - + -
155B ARG* 3.6 59.0 - - + +
156B GLU 5.4 0.9 - - - +
176B PRO* 4.7 1.3 - - + -
196B ASP 5.0 1.7 + - - +
197B GLN 3.4 0.8 - - - -
198B ARG* 1.3 79.4 - - - +
200B ASN* 1.3 70.1 + - - +
202B LEU* 3.3 10.2 + - - +
203B VAL* 3.2 37.7 + - + +
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Residues in contact with ASN 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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155B ARG* 2.7 45.0 + - - +
175B TYR* 5.0 1.6 + - - +
176B PRO* 3.7 23.6 - - - +
179B GLN* 2.8 42.8 + - + +
180B ALA* 5.1 0.3 - - - +
191B GLU* 5.0 0.5 - - - +
197B GLN* 3.3 15.3 + - - +
199B PHE* 1.3 83.4 - - - +
201B LEU* 1.3 64.0 + - - +
203B VAL* 3.2 8.0 + - - +
204B GLY* 3.2 16.6 + - - -
1433B TYE 4.1 8.9 + - - -
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Residues in contact with LEU 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B GLN* 3.7 12.6 - - - +
191B GLU* 3.4 56.1 - - + +
192B MET 4.0 13.5 - - - +
193B GLY* 4.2 0.7 - - - +
197B GLN* 3.1 25.1 + - + +
198B ARG* 3.3 5.1 + - - +
200B ASN* 1.3 74.9 - - - +
202B LEU* 1.3 61.9 + - - +
204B GLY 3.1 9.9 + - - -
205B ARG 3.3 3.8 + - - -
216B GLN* 3.1 18.9 + - - +
218B CYS* 3.6 24.0 - - + -
219B PHE 4.4 0.2 - - - +
220B LEU* 3.6 29.2 - - + -
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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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23B VAL* 4.7 16.8 - - + -
198B ARG* 3.1 46.2 + - + +
199B PHE* 3.6 10.8 - - + +
200B ASN 3.2 0.2 - - - -
201B LEU* 1.3 74.5 - - + +
203B VAL* 1.3 65.8 + - + +
205B ARG* 3.2 36.2 + - - +
206B GLU* 3.3 15.7 + - - +
218B CYS* 4.1 9.2 - - + -
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Residues in contact with VAL 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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147B MET* 3.7 29.8 - - + -
176B PRO* 4.2 15.7 - - + +
177B PHE* 4.5 9.6 - - + -
180B ALA* 3.9 15.7 - - + -
199B PHE* 3.2 43.7 + - + +
200B ASN* 3.2 9.6 + - - +
202B LEU* 1.3 76.8 - - - +
204B GLY* 1.3 63.4 + - - +
206B GLU* 3.1 8.8 + - + +
207B VAL* 2.9 30.6 + - + +
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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
----------------------------------------------------------
180B ALA* 3.6 25.2 - - - +
183B SER* 4.8 1.3 - - - -
191B GLU* 5.2 0.7 - - - -
200B ASN 3.2 5.9 + - - -
201B LEU 3.1 10.2 + - - -
203B VAL* 1.3 81.0 - - - +
205B ARG* 1.3 55.3 + - - +
207B VAL* 3.4 1.6 + - - +
208B GLN* 2.9 35.9 + - - +
216B GLN* 3.9 13.5 - - - -
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Residues in contact with ARG 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B VAL* 4.6 4.1 - - - +
24B PRO* 3.4 27.4 - - - +
27B GLU* 3.1 20.0 + - - -
201B LEU 3.3 2.4 + - - +
202B LEU* 3.2 24.6 + - + +
203B VAL 3.1 0.4 - - - -
204B GLY* 1.3 76.4 - - - +
206B GLU* 1.3 58.1 + - + +
208B GLN* 3.4 6.3 + - - +
209B ARG* 3.0 55.4 + - - +
215B PRO* 3.4 30.3 + - + +
216B GLN* 2.8 51.7 + - + +
218B CYS* 3.5 24.9 - - - -
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Residues in contact with GLU 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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146B LEU* 4.7 11.8 - - + +
147B MET* 5.6 11.2 - - + -
151B GLN* 6.2 1.8 - - - +
202B LEU 3.3 10.5 + - - +
203B VAL* 3.1 12.8 + - + +
205B ARG* 1.3 79.7 - - + +
207B VAL* 1.3 64.4 + - + +
209B ARG* 3.5 30.8 + - - +
210B ALA* 3.2 20.1 + - - +
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Residues in contact with VAL 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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143B LEU* 3.7 28.5 - - + -
146B LEU* 4.1 18.4 - - + -
177B PHE* 4.4 7.6 - - + -
180B ALA* 3.5 28.3 - - + +
181B TYR* 4.6 1.1 - - - +
184B VAL* 3.9 12.8 - - + -
203B VAL* 2.9 29.3 + - + +
204B GLY 3.9 1.8 - - - +
206B GLU* 1.3 77.4 - - + +
208B GLN* 1.3 64.5 + - - +
210B ALA* 3.1 2.3 + - - +
211B TYR* 3.0 33.9 + - + -
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Residues in contact with GLN 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B SER* 3.4 22.8 + - - -
184B VAL* 3.8 23.6 - - + -
188B ALA* 2.9 27.1 + - - +
204B GLY 2.9 17.7 + - - +
205B ARG 3.8 3.8 - - - +
207B VAL* 1.3 77.1 - - - +
209B ARG* 1.3 62.8 + - - +
211B TYR 3.0 8.1 + - - -
212B GLY 3.4 0.2 + - - -
213B GLN* 2.9 47.4 + - + +
214B SER 3.8 14.8 + - - +
215B PRO* 4.3 1.6 - - + -
216B GLN* 2.7 42.6 + - - +
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Residues in contact with ARG 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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205B ARG* 3.0 44.3 + - - +
206B GLU* 3.6 31.5 + - - +
208B GLN* 1.3 76.7 - - - +
210B ALA* 1.3 61.1 + - - +
211B TYR 3.2 0.9 + - - -
212B GLY* 3.2 13.0 + - - -
213B GLN 3.8 10.7 + - - +
215B PRO* 3.7 27.2 - - + +
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Residues in contact with ALA 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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146B LEU* 3.6 39.9 - - + -
206B GLU 3.2 7.1 + - - +
207B VAL 3.1 9.7 + - - +
209B ARG* 1.3 79.4 - - - +
211B TYR* 1.3 63.1 + - + +
212B GLY 3.4 1.5 + - - -
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Residues in contact with TYR 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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139B GLU* 4.3 12.3 + - - +
142B ARG* 5.0 6.4 - - + +
143B LEU* 3.7 28.2 + - + +
146B LEU* 4.7 7.2 - - + -
181B TYR* 4.0 22.5 - + - -
184B VAL* 4.0 28.5 - - + -
207B VAL* 3.0 44.6 + - + +
208B GLN 3.0 4.6 + - - +
210B ALA* 1.3 82.9 - - + +
212B GLY* 1.3 61.6 + - - +
213B GLN* 3.3 10.4 + - - +
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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