Contacts of the helix formed by residues 208 - 228 (chain B) in PDB entry 1H9T
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 VAL 208 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B THR* 3.9 21.8 - - - +
113B ILE* 5.0 5.6 - - + -
114B ARG* 4.4 26.2 - - + +
117B PHE* 5.0 9.6 - - + -
196B LEU* 4.9 17.0 - - + -
199B LEU* 5.2 4.0 - - + -
204B ALA 4.8 0.9 - - - +
205B HIS* 3.2 20.0 - - - +
206B ASP 3.1 4.0 + - - -
207B GLN* 1.3 79.4 - - - +
209B TYR* 1.3 70.4 + - - +
210B GLU* 2.9 5.1 + - - +
211B THR* 3.2 6.4 + - - +
212B VAL* 3.2 34.8 + - + +
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Residues in contact with TYR 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A ARG* 5.4 11.1 + - - -
107B ASN* 5.4 3.3 + - - -
110B THR* 3.9 32.1 + - + +
206B ASP 4.3 4.7 + - - +
208B VAL* 1.3 79.7 - - - +
210B GLU* 1.3 63.9 + - + +
213B ARG* 3.1 59.8 + - + +
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Residues in contact with GLU 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B ASP* 2.7 21.2 - - - +
207B GLN* 3.2 33.2 - - - +
208B VAL 3.4 15.3 - - - +
209B TYR* 1.3 74.7 - - + +
211B THR* 1.3 67.9 + - - +
213B ARG* 4.2 1.8 - - - +
214B ARG* 3.2 26.1 + - - +
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Residues in contact with THR 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B PHE* 3.2 34.3 - - + -
195B LYS* 4.5 27.7 - - + +
196B LEU* 5.3 7.6 - - + -
199B LEU* 5.9 1.9 - - - +
207B GLN 5.1 3.8 + - - -
208B VAL* 3.2 10.8 + - - -
210B GLU* 1.3 78.9 - - - +
212B VAL* 1.3 57.1 + - + +
214B ARG* 3.1 8.1 - - + +
215B TYR* 2.7 33.5 + - + +
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Residues in contact with VAL 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B ARG* 5.5 3.1 - - - +
106B THR* 3.7 14.1 - - + +
109B SER* 3.6 22.2 - - - +
110B THR* 3.6 26.2 - - + +
113B ILE* 4.8 6.1 - - + -
192B PHE* 4.8 16.2 - - + -
196B LEU* 6.0 2.5 - - + -
208B VAL* 3.2 32.0 + - + +
209B TYR 4.0 3.1 - - - +
211B THR* 1.3 74.0 - - + +
213B ARG* 1.3 67.2 + - - +
214B ARG 2.7 4.3 + - - -
215B TYR* 3.0 6.7 + - + +
216B GLY* 2.7 23.9 + - - -
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Residues in contact with ARG 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A ARG* 5.9 5.4 - - - +
118A ARG* 5.4 8.3 - - - +
103B SER* 5.5 2.8 + - - -
106B THR* 4.6 12.6 - - + +
107B ASN* 3.5 28.1 + - - +
110B THR* 5.7 0.4 - - + -
209B TYR* 3.1 59.7 + - + +
210B GLU* 4.2 2.0 - - - +
212B VAL* 1.3 79.1 - - + +
214B ARG* 1.3 63.2 + - - +
216B GLY* 3.6 1.3 + - - -
217B HIS* 3.1 61.5 + - + -
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Residues in contact with ARG 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B GLU* 3.2 17.8 + - - +
211B THR* 3.1 13.8 - - + +
212B VAL 2.7 0.8 + - - -
213B ARG* 1.3 73.0 - - - +
215B TYR* 1.3 57.4 + - + +
216B GLY 2.6 4.8 + - - -
217B HIS* 2.6 31.7 + - - +
218B GLU* 2.8 43.7 + - + +
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Residues in contact with TYR 215 (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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105B ARG* 5.0 13.0 - - - -
145B ASP* 4.3 10.6 + - - -
149B PHE* 4.8 10.3 - + - -
179B TYR* 4.8 3.9 + - - -
180B PHE* 4.8 5.0 - - - -
188B LEU* 4.0 28.7 - - + -
189B ALA* 3.7 25.4 - - - +
192B PHE* 3.3 56.7 - + + -
193B TYR* 4.8 0.6 + + - -
211B THR* 2.7 20.7 + - + +
212B VAL* 3.6 4.0 - - + +
214B ARG* 1.3 76.3 - - + +
216B GLY* 1.3 56.5 + - - +
218B GLU* 3.8 7.2 - - - -
219B SER* 2.8 46.2 + - - -
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Residues in contact with GLY 216 (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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105B ARG* 5.2 5.4 - - - -
106B THR* 4.0 23.8 - - - -
212B VAL 2.7 15.7 + - - -
213B ARG 3.9 2.5 - - - -
214B ARG 2.6 4.8 + - - -
215B TYR* 1.3 73.4 - - - +
217B HIS* 1.3 62.5 + - - -
219B SER* 3.1 5.0 + - - -
220B GLY* 2.9 21.0 + - - -
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Residues in contact with HIS 217 (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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213B ARG* 3.1 56.5 + - + -
214B ARG* 2.6 11.4 + - - +
216B GLY* 1.3 71.8 - - - -
218B GLU* 1.3 51.9 + - + +
220B GLY* 3.1 2.6 + - - -
221B GLU* 2.8 35.4 + - - +
224B HIS* 5.2 0.5 - - - -
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Residues in contact with GLU 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B LEU* 3.5 37.9 - - + +
214B ARG* 2.8 50.7 + - + +
215B TYR* 3.9 5.2 - - - +
217B HIS* 1.3 67.2 - - + +
219B SER* 1.3 69.4 + - - +
220B GLY 2.7 2.3 + - - -
221B GLU* 2.8 19.2 + - - +
222B ILE* 3.1 11.7 + - - +
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Residues in contact with SER 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B LEU* 5.9 2.1 - - - +
105B ARG* 4.5 11.6 + - - -
179B TYR* 3.1 32.9 - - - -
188B LEU* 3.7 7.2 - - - +
215B TYR* 2.8 44.5 + - - -
216B GLY* 3.1 6.9 + - - -
218B GLU* 1.3 73.9 - - - +
220B GLY* 1.3 72.9 + - - +
222B ILE* 3.1 6.8 + - - +
223B TRP* 3.0 17.5 + - - +
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Residues in contact with GLY 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B LEU* 5.8 6.1 - - - -
216B GLY 2.9 9.5 + - - -
217B HIS* 3.2 5.8 - - - -
218B GLU 2.7 2.2 + - - -
219B SER* 1.3 82.3 + - - +
221B GLU* 1.3 49.2 + - - -
223B TRP* 2.6 30.4 + - - +
224B HIS* 2.7 35.6 + - - -
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Residues in contact with GLU 221 (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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217B HIS 2.8 14.3 + - - +
218B GLU* 2.8 11.2 + - - +
220B GLY* 1.3 69.5 - - - -
222B ILE* 1.3 57.9 + - + +
224B HIS* 3.3 12.5 + - - +
225B ARG* 2.7 34.0 + - - +
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Residues in contact with ILE 222 (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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179B TYR* 3.7 23.8 - - + +
182B ASN* 5.9 0.4 - - + -
184B GLU* 3.4 46.4 - - + +
185B ALA* 4.2 10.1 - - + -
188B LEU* 3.7 29.2 - - + -
218B GLU 3.5 9.0 - - - +
219B SER* 3.1 7.2 - - - +
220B GLY 3.0 0.6 - - - -
221B GLU* 1.3 78.4 - - + +
223B TRP* 1.3 52.1 + - - +
225B ARG* 3.3 12.5 + - - +
226B MET* 2.7 37.1 - - + +
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Residues in contact with TRP 223 (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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95B PRO* 6.4 0.2 - - - +
98B ILE* 4.4 32.7 - - + +
99B ASP* 5.7 1.7 - - - +
102B LEU* 4.4 18.6 - - + -
175B ILE* 4.6 14.6 - - + -
178B HIS* 4.2 16.6 - + + -
179B TYR* 3.5 51.8 - + + -
219B SER 3.0 7.0 + - - +
220B GLY* 2.6 16.4 + - - +
222B ILE* 1.3 70.5 - - - +
224B HIS* 1.3 82.8 + + - +
225B ARG 3.1 1.1 - - - -
226B MET* 2.9 32.7 + - + +
227B GLN* 3.4 16.2 + - + +
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Residues in contact with HIS 224 (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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99B ASP* 3.0 28.9 + - - -
102B LEU* 6.5 0.7 - - + -
217B HIS 5.2 0.7 - - - -
220B GLY* 2.7 45.0 + - - +
221B GLU* 3.5 10.1 - - - +
223B TRP* 1.3 84.2 - + - +
225B ARG* 1.3 56.8 + - - +
226B MET 3.0 4.9 + - - -
227B GLN* 3.2 19.1 + - - +
228B LYS* 3.7 10.0 + - - +
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Residues in contact with ARG 225 (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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221B GLU 2.7 19.5 + - - +
222B ILE* 3.4 10.5 - - - +
223B TRP 3.1 0.4 - - - -
224B HIS* 1.3 75.2 - - - +
226B MET* 1.3 57.5 + - - +
227B GLN 3.6 0.2 - - - -
228B LYS* 5.2 1.8 - - - -
229B ASN* 4.0 10.6 + - - -
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Residues in contact with MET 226 (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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178B HIS 3.7 14.1 - - - +
179B TYR* 3.5 36.1 - - - +
181B ALA* 5.2 0.9 - - + -
182B ASN* 3.1 35.2 - - + +
184B GLU* 6.5 0.7 - - - -
222B ILE* 2.7 33.9 - - + +
223B TRP* 2.9 32.6 + - + +
225B ARG* 1.3 79.2 - - - +
227B GLN* 1.3 64.9 + - - +
229B ASN* 3.9 11.1 + - - +
230B LEU* 3.6 14.2 - - - +
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Residues in contact with GLN 227 (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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223B TRP* 3.4 16.7 + - + +
224B HIS* 3.2 12.3 + - - +
226B MET* 1.3 78.2 - - - +
228B LYS* 1.3 54.5 + - - +
229B ASN 2.3 21.8 + - - -
230B LEU* 3.3 21.0 + - - +
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Residues in contact with LYS 228 (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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224B HIS 3.7 8.9 + - - +
225B ARG* 5.2 1.5 - - - -
226B MET 3.9 0.4 - - - +
227B GLN* 1.3 72.1 - - - +
229B ASN* 1.3 70.4 + - - +
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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
------------------------------------------------------------
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