Contacts of the helix formed by residues 198 - 211 (chain B) in PDB entry 2CUY
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 MET 198 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118B MET* 3.5 52.7 - - + +
121B ALA* 4.0 11.4 - - + -
191B ALA* 4.5 1.3 - - + -
192B PRO* 3.2 49.6 - - - +
193B PHE* 3.9 11.4 - - + -
194B HIS 3.6 13.5 - - - +
195B SER 2.9 12.9 + - - +
197B LEU* 1.3 77.2 - - - +
199B ALA* 1.3 65.8 + - - +
200B PRO* 3.3 3.1 - - - -
201B ALA* 2.8 21.0 + - + +
202B ARG 3.3 3.8 + - - -
244B ILE* 3.7 20.6 - - + +
245B THR* 3.7 2.7 - - + -
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Residues in contact with ALA 199 (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 SER 3.2 15.6 + - - +
198B MET* 1.3 76.5 - - - +
200B PRO* 1.3 72.1 - - + +
202B ARG* 2.9 37.4 + - - +
203B LYS* 3.0 26.3 + - - +
245B THR* 3.4 11.9 - - + +
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Residues in contact with PRO 200 (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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121B ALA* 3.9 30.1 - - + +
197B LEU 3.5 12.3 - - - +
198B MET 3.5 1.1 - - - -
199B ALA* 1.3 94.8 - - + +
201B ALA* 1.3 59.6 + - - +
203B LYS* 4.1 12.3 - - + +
204B ARG* 3.2 31.7 + - - +
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Residues in contact with ALA 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B TYR* 3.7 41.0 - - + +
118B MET* 3.8 19.1 - - + +
121B ALA* 4.4 3.8 - - + +
198B MET* 2.8 18.4 + - + +
200B PRO* 1.3 73.1 - - - +
202B ARG* 1.3 65.4 - - - +
204B ARG* 3.4 3.6 + - - +
205B LEU* 3.1 25.5 + - - +
244B ILE* 4.3 7.8 - - + +
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Residues in contact with ARG 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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198B MET 3.3 4.5 + - - +
199B ALA* 2.9 32.5 + - - +
201B ALA* 1.3 77.2 - - - +
203B LYS* 1.3 80.5 + - - +
205B LEU* 3.3 3.1 + - - +
206B ALA* 3.1 23.2 + - + +
241B LEU* 3.4 39.8 - - + +
242B GLU* 4.5 9.1 + - - +
244B ILE* 3.7 18.3 - - + +
245B THR* 2.8 37.4 + - + +
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Residues in contact with LYS 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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199B ALA* 3.0 27.4 + - - +
200B PRO* 4.1 8.7 - - + +
202B ARG* 1.3 99.4 - - - +
204B ARG* 1.3 63.5 + - + +
206B ALA* 3.5 17.5 - - - +
207B GLU* 4.2 2.9 + - - +
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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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117B TYR* 3.4 46.5 + - + +
120B GLU* 2.7 50.7 + - - +
200B PRO* 3.2 19.7 + - + +
201B ALA 3.8 3.4 - - - +
202B ARG 3.2 0.8 - - - -
203B LYS* 1.3 75.9 - - + +
205B LEU* 1.3 65.1 + - - +
206B ALA 3.1 2.5 + - - -
207B GLU* 3.3 15.3 + - - +
208B ASP* 3.5 10.6 - - - +
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Residues in contact with LEU 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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93B TRP* 3.7 31.6 - - + -
110B LEU* 3.7 37.5 - - + +
113B LEU* 4.5 2.7 - - + -
114B ARG* 4.2 17.9 - - + +
117B TYR* 3.6 21.4 - - + -
201B ALA 3.1 17.2 + - - +
202B ARG 4.0 2.9 - - - +
204B ARG* 1.3 74.6 - - - +
206B ALA* 1.3 66.3 + - - +
207B GLU 3.1 0.5 + - - -
208B ASP* 3.1 4.8 + - + -
209B LEU* 2.9 24.4 + - + +
241B LEU* 3.9 11.4 - - + -
244B ILE* 3.9 21.5 - - + -
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Residues in contact with ALA 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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202B ARG* 3.1 13.0 + - + +
203B LYS* 3.5 17.3 - - - +
204B ARG 3.1 0.4 - - - -
205B LEU* 1.3 76.8 - - - +
207B GLU* 1.3 61.5 + - - +
209B LEU* 4.0 1.5 - - - +
210B ALA* 3.1 23.4 + - - +
241B LEU* 3.6 28.6 - - + +
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Residues in contact with GLU 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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203B LYS 4.2 3.0 + - - +
204B ARG 3.3 10.9 + - - +
205B LEU 3.1 0.6 - - - -
206B ALA* 1.3 77.4 - - - +
208B ASP* 1.3 70.4 + - - +
210B ALA* 3.1 19.6 + - + +
211B GLN* 3.6 23.5 + - - +
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Residues in contact with ASP 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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110B LEU* 3.8 20.3 - - + +
113B LEU* 3.5 22.2 - - + +
117B TYR* 2.7 36.3 + - - -
204B ARG 3.5 6.6 - - - +
205B LEU* 3.1 6.8 + - + +
207B GLU* 1.3 79.4 - - - +
209B LEU* 1.3 62.4 + - - +
211B GLN* 3.2 27.1 + - - +
212B VAL* 3.7 11.4 - - - +
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Residues in contact with LEU 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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93B TRP* 4.0 21.5 - - + -
102B LEU* 5.5 0.2 - - + -
110B LEU* 3.6 27.7 - - + +
205B LEU* 2.9 19.6 + - + +
206B ALA* 4.1 3.6 - - - +
208B ASP* 1.3 77.5 - - - +
210B ALA* 1.3 60.5 + - - +
211B GLN 3.1 0.2 - - - -
212B VAL* 3.2 12.4 + - + +
214B LEU* 4.8 13.5 - - + -
237B ARG* 2.9 64.0 + - + +
240B LEU* 4.2 10.1 - - + -
241B LEU* 3.8 20.9 - - + -
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Residues in contact with ALA 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B ALA 3.1 17.5 + - - +
207B GLU* 3.1 16.3 + - + +
209B LEU* 1.3 76.0 - - - +
211B GLN* 1.3 60.6 + - + +
212B VAL 3.3 1.1 + - - +
237B ARG* 4.3 15.9 + - - +
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Residues in contact with GLN 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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207B GLU* 3.7 28.2 + - + +
208B ASP* 3.2 16.8 + - - +
209B LEU 3.1 1.0 - - - -
210B ALA* 1.3 81.1 - - + +
212B VAL* 1.3 61.9 + - + +
213B PRO* 3.9 5.9 - - - +
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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