Contacts of the helix formed by residues 203 - 215 (chain B) in PDB entry 3UVH
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
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Residue Dist Surf HB Arom Phob DC
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134B LEU* 3.5 17.9 - - + -
137B LEU* 3.5 29.6 - - + -
138B LYS* 3.5 47.6 - - + -
141B ASP* 3.0 24.5 - - + +
199B ILE* 4.1 16.8 - - + -
200B PRO* 2.9 42.5 + - + +
201B GLU 3.6 2.9 - - - -
202B ALA* 1.3 81.1 - - + +
204B ARG* 1.3 58.6 + - - +
206B VAL* 3.2 6.4 + - + -
207B HIS* 3.1 22.2 + - - -
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Residues in contact with ARG 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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141B ASP* 3.4 1.4 + - - -
145B THR* 6.0 0.2 - - + -
159B ASP* 3.5 31.7 + - - -
162B VAL* 5.0 12.4 - - - +
201B GLU 3.8 13.5 - - - +
202B ALA* 2.9 17.8 + - - +
203B PHE* 1.3 72.1 - - - +
205B GLY* 1.3 58.4 + - - +
207B HIS* 3.4 4.5 + - - +
208B ARG* 2.9 43.4 + - + +
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Residues in contact with GLY 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B ASP* 3.0 10.2 + - - -
144B LEU* 3.7 14.5 - - - +
145B THR* 3.7 26.5 - - - +
204B ARG* 1.3 80.1 - - - +
206B VAL* 1.3 61.1 + - - +
208B ARG* 4.0 12.2 - - - +
209B TYR* 3.0 23.7 + - - +
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Residues in contact with VAL 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B LEU* 3.7 18.2 - - + +
140B LEU* 3.9 21.5 - - + -
141B ASP* 3.2 35.6 + - + +
144B LEU* 3.9 5.8 - - + -
184B LEU* 5.2 4.0 - - + -
199B ILE* 3.9 28.3 - - + -
203B PHE* 3.8 11.2 - - + +
205B GLY* 1.3 74.4 - - - +
207B HIS* 1.3 62.2 + - - +
209B TYR* 3.2 5.0 - - + +
210B LEU* 3.1 36.6 + - + +
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Residues in contact with HIS 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B GLN* 4.8 11.8 + - - -
198B THR* 6.2 0.4 - - - -
199B ILE* 2.6 46.0 + - + +
200B PRO 3.2 16.2 + - - -
201B GLU* 3.5 29.7 + - - +
203B PHE 3.1 21.9 + - - +
204B ARG* 4.1 5.4 - - - +
206B VAL* 1.3 74.1 - - - +
208B ARG* 1.3 55.3 + - - +
210B LEU* 4.0 11.9 - - + +
211B SER* 2.5 38.5 + - - +
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Residues in contact with ARG 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B LEU* 4.6 5.1 + - - +
145B THR* 4.0 22.6 - - - +
162B VAL* 4.3 4.8 - - - +
163B SER 2.9 26.5 + - - -
164B GLN* 4.0 26.4 + - - +
165B ARG 3.6 22.8 + - - -
166B LYS 5.0 0.2 - - - -
204B ARG* 2.9 32.0 + - + +
205B GLY* 4.0 6.4 + - - +
207B HIS* 1.3 69.3 - - + +
209B TYR* 1.3 66.9 + - - +
211B SER* 3.7 6.3 - - - -
212B ASN* 3.0 36.4 + - - +
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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
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140B LEU* 5.0 0.4 - - + -
144B LEU* 3.8 25.4 - - + -
166B LYS 3.8 19.5 - - - +
167B PHE* 3.8 19.1 - + - -
168B LEU* 3.6 20.7 - - + +
177B ASP* 2.6 33.3 + - - -
180B LEU* 3.8 22.7 - - + +
181B LEU* 3.5 34.8 - - + +
184B LEU* 3.9 15.9 - - + -
205B GLY 3.0 13.4 + - - +
206B VAL* 3.2 10.8 - - - +
208B ARG* 1.3 78.5 - - - +
210B LEU* 1.3 59.0 + - - +
212B ASN* 3.6 1.9 - - - +
213B ALA* 2.8 29.8 + - - +
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Residues in contact with LEU 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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181B LEU* 4.3 13.0 - - + -
184B LEU* 3.9 35.4 - - + -
185B HIS 5.7 0.2 - - - +
188B GLN* 4.0 30.3 - - + +
199B ILE* 4.2 16.2 - - + -
206B VAL* 3.1 23.5 + - + +
207B HIS* 4.0 12.3 - - - +
209B TYR* 1.3 78.6 - - + +
211B SER* 1.3 60.8 + - - +
213B ALA* 4.1 3.8 - - - -
214B TYR* 2.8 56.7 + - + +
219B PHE* 5.7 1.6 - - + -
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Residues in contact with SER 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B HIS* 2.5 26.3 + - - +
208B ARG* 3.7 7.6 - - - -
209B TYR 3.3 0.2 - - - -
210B LEU* 1.3 77.3 - - - +
212B ASN* 1.3 64.9 + - - +
214B TYR* 3.3 5.3 + - - +
215B ALA* 3.2 24.3 + - - +
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Residues in contact with ASN 212 (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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164B GLN 5.8 0.2 + - - -
165B ARG 4.7 1.4 + - - -
166B LYS* 3.4 46.4 + - - +
167B PHE* 3.6 19.7 - - + -
208B ARG* 3.0 26.1 + - - +
209B TYR 3.6 3.8 - - - +
211B SER* 1.3 81.7 - - - +
213B ALA* 1.3 60.3 + - - +
215B ALA* 3.4 14.8 + - - +
216B ARG* 3.5 18.7 + - - +
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Residues in contact with ALA 213 (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 PHE* 3.9 8.8 - - + -
173B LEU* 5.6 0.9 - - - -
181B LEU* 3.5 38.4 - - + -
209B TYR* 2.8 19.0 + - + +
210B LEU* 3.6 5.8 - - - +
212B ASN* 1.3 73.7 - - - +
214B TYR* 1.3 64.5 + - - +
216B ARG* 3.0 20.1 + - - +
219B PHE* 3.2 25.2 - - + +
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Residues in contact with TYR 214 (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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185B HIS* 2.8 43.7 + + - +
188B GLN* 3.2 23.7 + - - -
189B VAL* 5.7 0.2 - - - +
210B LEU* 2.8 54.5 + - + +
211B SER* 3.3 4.2 + - - +
213B ALA* 1.3 71.9 - - - +
215B ALA* 1.3 58.7 + - - +
216B ARG 3.1 2.5 + - - -
219B PHE* 3.1 29.4 - + - -
220B ALA* 3.6 23.6 - - + +
223B CYS* 4.5 5.2 - - - -
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Residues in contact with ALA 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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211B SER 3.2 15.6 + - - +
212B ASN* 3.7 8.3 - - - +
213B ALA 3.1 1.0 - - - -
214B TYR* 1.3 77.0 - - - +
216B ARG* 1.3 63.0 + - + +
217B GLU 4.0 1.4 + - - -
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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