Contacts of the helix formed by residues 201 - 209 (chain B) in PDB entry 1P5Q
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 PRO 201 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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199B ASP 3.6 4.0 - - - +
200B LEU* 1.3 86.3 - - + +
202B TYR* 1.3 67.7 + - - +
204B LEU* 2.9 29.4 + - + +
205B GLU* 3.7 3.1 + - - +
221B LEU* 3.8 5.2 - - + -
225B TYR 3.8 6.5 - - - +
226B ALA* 3.7 26.0 - - - +
227B PHE* 4.0 17.9 - - + -
245B TYR* 2.9 49.6 - - + +
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Residues in contact with TYR 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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196B GLU* 6.1 1.0 - - - +
200B LEU 3.4 3.5 + - - -
201B PRO* 1.3 70.9 - - - +
203B GLY* 1.3 63.7 + - - +
205B GLU* 3.3 21.3 + - + +
206B ARG* 2.7 54.0 + - + -
224B SER 4.8 7.6 - - - -
225B TYR* 3.7 30.0 + + - +
226B ALA 4.3 5.1 + - - +
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Residues in contact with GLY 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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150B ILE* 3.7 12.7 - - - +
201B PRO 3.0 0.6 + - - -
202B TYR* 1.3 81.7 - - - +
204B LEU* 1.3 62.0 + - - +
206B ARG* 3.1 18.3 + - - +
207B ALA* 3.2 11.6 + - - +
221B LEU* 3.7 17.3 - - - +
225B TYR* 3.1 24.4 + - - -
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Residues in contact with LEU 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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174B LEU* 4.4 8.5 - - + -
200B LEU* 3.4 34.1 - - + -
201B PRO* 2.9 24.2 + - + +
203B GLY* 1.3 71.4 - - - +
205B GLU* 1.3 63.2 + - + +
207B ALA* 3.1 7.3 + - + +
208B ILE* 3.0 30.0 + - + +
219B VAL* 3.9 22.4 - - + -
221B LEU* 3.8 11.2 - - + +
245B TYR* 3.9 26.9 - - + -
247B LEU* 3.7 27.6 - - + -
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Residues in contact with GLU 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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190B PHE* 3.9 9.5 - - + -
192B ILE* 3.6 15.2 - - + +
193B GLY* 2.7 35.4 + - - -
194B GLU 4.2 0.7 + - - -
195B GLY* 2.8 38.5 + - - -
196B GLU* 3.3 8.0 + - - +
200B LEU* 4.2 8.0 - - + +
201B PRO 4.3 6.7 - - - +
202B TYR* 3.3 14.9 + - + +
203B GLY 3.3 0.8 - - - -
204B LEU* 1.3 76.7 - - + +
206B ARG* 1.3 59.1 + - - +
207B ALA 3.0 1.4 + - - -
208B ILE* 3.3 12.0 + - - +
209B GLN* 3.0 32.1 + - - +
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Residues in contact with ARG 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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145B GLU 5.8 0.4 - - - -
146B GLU* 2.6 38.9 + - - +
150B ILE* 3.7 20.3 - - + +
202B TYR* 2.7 43.7 + - - +
203B GLY* 3.1 15.2 + - - +
205B GLU* 1.3 79.0 - - - +
207B ALA* 1.3 57.5 + - - +
209B GLN* 4.0 19.0 + - - +
210B ARG* 3.6 26.9 + - - +
225B TYR* 3.8 15.7 + - - -
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Residues in contact with ALA 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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150B ILE* 4.0 8.7 - - + -
152B ARG* 3.3 25.3 + - + +
203B GLY 3.2 9.4 + - - +
204B LEU* 3.1 14.8 + - + +
205B GLU 3.0 0.4 - - - -
206B ARG* 1.3 77.1 - - - +
208B ILE* 1.3 59.6 + - - +
209B GLN 2.9 1.3 - - - -
210B ARG* 2.7 24.0 + - - +
211B MSE 3.3 7.5 + - - +
219B VAL* 3.9 28.7 - - + -
247B LEU* 5.8 0.2 - - + -
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Residues in contact with ILE 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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164B PRO* 3.7 9.1 - - + +
170B VAL* 4.2 16.6 - - + -
172B VAL* 4.6 10.8 - - + -
174B LEU* 5.9 0.9 - - + -
190B PHE* 3.7 32.5 - - + -
192B ILE* 3.8 17.3 - - + -
200B LEU* 5.4 0.4 - - + -
204B LEU* 3.0 26.8 + - + +
205B GLU* 3.7 9.6 - - + +
207B ALA* 1.3 75.4 - - - +
209B GLN* 1.3 57.4 + - - +
211B MSE 2.8 32.3 + - - +
247B LEU* 3.4 28.9 - - + -
249B LEU* 4.3 15.0 - - + -
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Residues in contact with GLN 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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163B LYS* 3.2 25.3 - - - +
164B PRO* 3.3 23.7 + - - +
165B ASN* 4.0 1.8 - - - +
166B GLU* 3.2 41.5 - - - +
192B ILE* 3.4 28.3 - - + +
205B GLU* 3.0 18.2 + - - +
206B ARG* 4.0 18.4 + - - +
207B ALA 2.9 0.8 - - - -
208B ILE* 1.3 76.5 - - - +
210B ARG* 1.3 59.5 + - + +
211B MSE 3.2 0.7 - - - -
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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