Contacts of the strand formed by residues 203 - 211 (chain B) in PDB entry 1HYH
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 PHE 203 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194B ASN* 3.1 9.5 - - - -
195B LEU* 2.8 67.4 + - + -
196B GLY 4.4 0.9 - - - -
201B SER 3.7 12.3 - - - +
202B GLN* 1.3 78.2 - - - +
204B VAL* 1.3 69.2 + - - +
205B ALA* 4.2 12.1 - - + -
231B GLU* 4.8 6.5 - - - +
307B GLU* 3.5 44.6 - - + -
310B LYS* 3.7 43.5 - - + +
311B LEU* 3.8 17.0 - - + -
314B SER* 4.5 1.1 - - - -
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Residues in contact with VAL 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B MET* 3.8 22.0 - - + -
193B TYR 4.3 0.9 - - - +
194B ASN* 3.4 29.2 - - - +
202B GLN* 5.6 0.4 - - - +
203B PHE* 1.3 80.0 - - - +
205B ALA* 1.3 61.1 + - - +
206B TRP* 2.9 63.1 + - + +
209B VAL* 4.1 10.3 - - + -
231B GLU* 3.7 23.6 + - + +
234B ALA* 5.2 4.9 - - + -
307B GLU* 4.4 1.7 - - - +
310B LYS* 5.5 2.6 + - - -
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Residues in contact with ALA 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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193B TYR 3.0 15.5 + - - +
195B LEU* 3.6 30.7 - - + -
203B PHE* 3.7 8.2 + - + -
204B VAL* 1.3 70.0 - - - +
206B TRP* 1.3 49.0 + - - +
207B SER 3.1 4.7 - - - -
208B THR* 2.6 53.9 + - + +
209B VAL* 3.7 2.1 + - - +
303B LEU* 4.1 1.6 - - + -
307B GLU* 3.4 19.7 - - - -
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Residues in contact with TRP 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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175B MET* 4.5 3.8 - - + -
179B VAL* 4.2 16.6 - - + -
204B VAL* 2.9 45.0 + - + +
205B ALA* 1.3 68.4 - - - +
207B SER* 1.3 59.6 + - - +
208B THR 3.3 0.4 - - - -
209B VAL* 3.6 16.6 + - + +
215B PRO* 6.1 0.3 - - - +
216B ILE* 3.4 39.7 - - + +
217B VAL* 3.4 30.1 + - + +
227B LEU* 3.6 47.0 - - + +
230B ILE* 3.9 24.9 - - + -
231B GLU* 3.2 39.3 + - + -
307B GLU* 3.2 6.0 + - - +
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Residues in contact with SER 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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205B ALA 2.9 0.6 + - - -
206B TRP* 1.3 78.0 - - - +
208B THR* 1.3 68.2 + - - +
209B VAL 3.4 3.2 - - - +
215B PRO* 5.6 4.7 - - - +
217B VAL* 4.7 7.6 - - - +
302B ASP 4.2 13.2 + - - -
303B LEU* 4.4 0.5 - - - -
304B THR* 4.0 15.3 - - - -
307B GLU* 2.5 33.5 + - - -
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Residues in contact with THR 208 (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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191B SER* 3.7 4.0 + - - +
192B GLY* 3.2 13.0 + - - -
193B TYR* 3.1 49.1 + - + -
205B ALA* 2.6 33.5 + - + +
207B SER* 1.3 82.9 - - - +
209B VAL* 1.3 60.0 + - - +
210B ARG* 3.7 7.0 + - - +
301B LEU* 4.3 17.0 - - + -
302B ASP 6.0 1.6 - - - +
303B LEU* 4.3 5.6 - - + -
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Residues in contact with VAL 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B MET* 3.8 33.9 - - + -
179B VAL* 4.8 0.7 - - + -
190B VAL* 4.3 8.3 - - + -
191B SER 3.0 12.3 - - - +
192B GLY* 3.9 4.3 - - - -
193B TYR 4.5 0.2 - - - +
204B VAL* 4.1 4.9 - - + -
205B ALA 3.9 13.7 - - - +
206B TRP* 3.6 24.3 + - + +
207B SER 3.4 3.4 - - - +
208B THR* 1.3 76.8 - - - +
210B ARG* 1.3 66.1 + - - +
215B PRO* 3.9 3.6 - - - +
216B ILE* 3.1 52.0 + - + +
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Residues in contact with ARG 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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210A ARG* 4.8 20.5 - - - +
189B SER 4.3 1.6 - - - +
190B VAL* 4.0 1.0 - - - -
191B SER* 2.9 47.3 + - - +
208B THR 4.2 6.7 + - - +
209B VAL* 1.3 78.8 - - - +
211B VAL* 1.3 65.7 + - - +
213B GLY* 3.4 29.3 + - - +
214B GLN* 3.1 23.4 - - - +
215B PRO* 4.0 17.4 - - + +
216B ILE 3.9 2.2 - - - +
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Residues in contact with VAL 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B VAL* 3.6 28.9 - - + -
183B PHE* 4.0 21.1 - - + -
185B LEU* 3.8 15.3 - - + -
189B SER 4.7 3.4 - - - -
190B VAL* 3.7 18.6 - - + -
209B VAL* 5.2 0.4 - - + -
210B ARG* 1.3 79.6 - - - +
212B MET* 1.3 73.4 + - + +
213B GLY 3.3 1.8 - - - -
214B GLN* 2.9 21.2 + - - +
216B ILE* 4.1 9.9 - - + -
219B LEU* 3.5 25.9 - - + +
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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