Contacts of the helix formed by residues 201 - 211 (chain B) in PDB entry 1R88
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 ALA 201 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196B ASN* 3.6 21.5 + - - +
199B TRP 4.6 1.6 - - - +
200B GLY* 1.3 71.2 - - - -
202B PRO* 1.3 73.4 - - + +
203B GLN* 3.1 20.9 + - - +
204B LEU* 3.1 35.8 + - + +
205B GLY 4.3 1.0 + - - -
206B ARG 5.2 0.2 + - - -
207B TRP* 4.7 0.2 - - - -
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Residues in contact with PRO 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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180B ASN* 3.5 39.5 - - - +
196B ASN* 3.8 10.8 - - - +
200B GLY 3.3 4.5 - - - +
201B ALA* 1.3 82.9 - - + +
203B GLN* 1.3 80.4 + - - +
204B LEU 3.2 0.7 - - - -
205B GLY* 3.2 15.0 + - - -
207B TRP* 3.7 33.2 - - + +
208B LYS* 5.9 0.9 + - - -
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Residues in contact with GLN 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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201B ALA* 3.1 19.4 + - + +
202B PRO* 1.3 99.9 - - - +
204B LEU* 1.3 63.9 + - + +
205B GLY* 3.2 1.5 + - - -
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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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200B GLY* 4.8 0.2 - - - -
201B ALA* 3.1 31.5 + - + +
203B GLN* 1.3 81.6 - - + +
205B GLY* 1.3 58.4 + - - +
206B ARG* 3.5 45.8 + - + +
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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
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201B ALA 4.3 0.2 + - - -
202B PRO 3.2 12.2 + - - -
203B GLN 3.2 5.0 - - - -
204B LEU* 1.3 78.2 - - - +
206B ARG* 1.3 63.2 + - - +
207B TRP* 3.3 4.1 + - - -
208B LYS* 3.5 35.2 + - - +
209B TRP* 4.0 8.0 + - - -
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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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109B GLU* 2.9 40.4 + - - +
199B TRP* 3.4 15.4 + - + +
200B GLY* 3.6 15.8 - - - -
201B ALA 5.2 0.8 + - - -
204B LEU* 3.5 36.9 + - + +
205B GLY* 1.3 74.9 - - - +
207B TRP* 1.3 64.9 + - - +
208B LYS 3.2 2.2 - - - -
209B TRP* 3.2 57.1 + - + +
210B HIS* 3.1 22.3 - - - +
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Residues in contact with TRP 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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174B PRO 3.5 18.8 - - - -
175B SER* 3.6 16.3 + - - +
180B ASN* 3.6 39.0 - - + +
183B ILE* 4.3 17.5 - - + -
184B ALA* 5.4 0.4 - - + -
195B THR* 3.9 38.4 - - - -
198B MET* 4.1 13.5 - - + -
199B TRP* 3.6 50.9 - + + +
200B GLY 3.0 20.1 + - - -
201B ALA 4.7 0.2 - - - -
202B PRO* 3.7 34.7 - - + +
205B GLY 3.3 0.8 - - - -
206B ARG* 1.3 77.3 - - - +
208B LYS* 1.3 62.2 + - - +
210B HIS* 3.3 13.9 + - - +
211B ASP* 3.6 11.4 + - - +
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Residues in contact with LYS 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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175B SER* 3.8 30.1 + - - +
205B GLY* 3.5 23.3 + - - +
207B TRP* 1.3 77.8 - - - +
209B TRP* 1.3 62.6 + - + +
210B HIS 3.2 0.5 + - - -
211B ASP* 3.3 8.2 + - - +
214B VAL* 3.9 18.7 - - + +
215B HIS* 3.0 25.1 + - - +
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Residues in contact with TRP 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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109B GLU* 5.5 1.1 - - - -
157B PHE* 3.3 21.5 - - - -
205B GLY 4.0 13.0 + - - -
206B ARG* 3.2 52.2 + - + +
208B LYS* 1.3 78.8 - - + +
210B HIS* 1.3 76.1 + + + +
215B HIS* 3.8 9.0 + - - -
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Residues in contact with HIS 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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106B THR* 3.9 8.2 + - - -
107B ASN* 5.0 6.1 - - + -
109B GLU* 5.2 4.2 + - - -
149B TYR* 2.7 41.7 + - - +
153B ALA* 4.0 0.3 - - - +
157B PHE* 3.6 19.4 - - + -
199B TRP* 3.3 50.5 + + + +
206B ARG* 3.1 27.8 + - - +
207B TRP 3.3 2.8 + - - +
208B LYS 3.2 0.8 - - - -
209B TRP* 1.3 93.7 - + + +
211B ASP* 1.3 59.8 + - - +
212B PRO* 3.6 1.6 - - - +
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Residues in contact with ASP 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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157B PHE* 4.0 2.0 - - - -
172B LEU 3.5 2.3 - - - +
173B TYR* 3.3 9.1 - - - -
174B PRO* 3.3 11.5 - - + +
175B SER* 2.6 38.1 + - - +
207B TRP 3.6 10.3 - - - +
208B LYS 3.3 14.7 + - - +
209B TRP 3.4 1.4 + - - -
210B HIS* 1.3 74.9 - - - +
212B PRO* 1.3 62.5 - - - +
213B TRP* 2.8 26.3 + - - +
214B VAL* 3.3 12.7 + - + -
215B HIS* 3.0 30.3 + - - +
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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