Contacts of the helix formed by residues 196 - 211 (chain B) in PDB entry 7CR3
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 196 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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182B VAL* 4.5 18.9 - - + +
195B SER* 1.3 76.0 - - - +
197B LEU* 1.3 67.0 + - + +
198B ARG 3.4 1.3 - - - -
199B SER* 2.5 36.3 + - - +
200B LEU* 3.1 5.7 + - - +
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Residues in contact with LEU 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B SER* 5.5 7.2 - - - +
126B LEU* 5.5 7.0 - - + -
127B TYR* 6.4 1.8 - - + -
195B SER* 3.1 9.8 - - - +
196B ALA* 1.3 84.1 - - + +
198B ARG* 1.3 63.3 + - + +
200B LEU* 2.9 45.2 + - + +
201B ARG* 3.1 13.2 + - - +
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Residues in contact with ARG 198 (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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195B SER* 4.1 30.9 + - - +
196B ALA 3.4 0.2 - - - -
197B LEU* 1.3 75.2 - - + +
199B SER* 1.3 62.9 + - - +
201B ARG* 3.1 31.0 - - - +
202B PHE* 3.0 38.9 + - + -
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Residues in contact with SER 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B VAL* 4.7 12.1 - - - +
195B SER 5.0 0.2 + - - -
196B ALA* 2.5 33.9 + - - +
197B LEU 3.2 0.4 - - - -
198B ARG* 1.3 78.2 - - - +
200B LEU* 1.3 57.7 + - - +
202B PHE* 3.6 8.0 - - - +
203B LEU* 2.9 36.7 + - - +
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Residues in contact with LEU 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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110B SER* 3.9 17.0 - - - -
113B SER* 6.0 1.1 - - - +
126B LEU* 4.7 14.8 - - + -
130B GLU* 5.3 13.0 - - + -
182B VAL* 5.4 13.7 - - + -
183B LEU* 6.4 1.8 - - + -
196B ALA 3.1 4.6 + - - +
197B LEU* 2.9 37.6 + - + +
199B SER* 1.3 81.6 + - - +
201B ARG* 1.3 59.9 + - + +
203B LEU* 3.2 9.9 + - - +
204B GLN* 2.9 57.1 + - + +
207B ARG* 4.5 3.5 + - - +
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Residues in contact with ARG 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A PHE* 3.4 32.3 - - - -
251A TYR* 4.5 15.8 + - - -
252A LEU* 4.6 4.2 - - - +
264A TYR* 4.2 35.1 - - - +
110B SER* 5.3 5.2 - - - +
114B THR* 5.5 5.9 + - - -
197B LEU 3.1 9.2 + - - +
198B ARG* 3.1 43.4 + - - +
200B LEU* 1.3 83.9 - - + +
202B PHE* 1.3 69.4 + - + +
204B GLN* 3.2 11.3 + - - +
205B ILE* 3.0 33.6 + - + +
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Residues in contact with PHE 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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248A PHE* 3.6 39.7 - + - -
198B ARG* 3.0 37.4 + - + +
199B SER* 3.6 9.0 - - - +
201B ARG* 1.3 86.0 - - + +
203B LEU* 1.3 62.3 + - + +
205B ILE* 3.2 18.4 + - + +
206B LEU* 3.0 21.1 + - - +
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Residues in contact with LEU 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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174B MET* 6.0 2.5 - - + -
175B VAL* 3.9 22.8 - - + +
178B ALA* 4.1 24.0 - - + -
179B SER* 4.4 9.4 - - - +
182B VAL* 4.5 14.6 - - + -
199B SER* 2.9 23.4 + - - +
200B LEU* 3.2 4.9 + - - +
202B PHE* 1.3 77.3 - - + +
204B GLN* 1.3 57.1 + - - +
206B LEU* 3.3 22.5 + - + +
207B ARG* 2.9 51.9 + - - +
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Residues in contact with GLN 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B VAL* 5.2 2.2 - - + +
106B CYS* 2.9 32.2 - - - -
107B LEU* 3.3 22.7 - - + +
110B SER* 2.4 33.0 + - - -
126B LEU* 4.5 2.8 - - - +
130B GLU* 5.9 1.4 - - - +
200B LEU* 2.9 43.8 + - + +
201B ARG* 3.2 10.5 + - - +
203B LEU* 1.3 74.8 - - - +
205B ILE* 1.3 59.2 + - - +
207B ARG* 3.2 26.4 - - - +
208B MET* 2.9 29.7 + - - +
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Residues in contact with ILE 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A LEU* 5.4 4.9 - - + -
244A ILE* 3.8 41.7 - - + -
248A PHE* 5.9 7.6 - - + -
264A TYR* 5.0 5.2 - - + +
107B LEU* 5.1 6.5 - - + -
201B ARG* 3.0 22.1 + - + +
202B PHE* 3.2 17.2 + - + +
204B GLN* 1.3 77.2 - - + +
206B LEU* 1.3 63.7 + - - +
208B MET* 3.2 7.6 + - + +
209B ILE* 3.0 35.7 + - + +
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Residues in contact with LEU 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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171B ILE* 4.5 17.5 - - + -
174B MET* 4.3 20.2 - - + -
175B VAL* 4.0 30.5 - - + -
202B PHE 3.0 13.0 + - - +
203B LEU* 3.4 21.1 - - + +
204B GLN 3.2 0.2 - - - -
205B ILE* 1.3 77.0 - - - +
207B ARG* 1.3 62.5 + - - +
209B ILE* 3.1 11.6 + - - +
210B ARG* 2.9 27.9 + - + +
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Residues in contact with ARG 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B VAL* 3.8 29.0 - - + +
106B CYS* 5.1 5.7 - - - -
130B GLU* 5.2 8.3 - - - +
133B THR* 4.8 13.1 - - - +
134B ILE* 5.7 4.6 - - - +
137B PHE* 4.2 27.6 - - + -
175B VAL* 4.2 23.1 - - + +
179B SER* 4.5 15.0 + - - -
200B LEU* 4.5 4.6 + - - +
203B LEU* 2.9 50.2 + - - +
204B GLN* 3.2 34.9 - - - +
206B LEU* 1.3 79.2 - - + +
208B MET* 1.3 61.8 + - - +
210B ARG* 3.2 25.9 - - + +
211B MET* 3.7 5.0 + - - +
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Residues in contact with MET 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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237A TYR* 5.1 11.6 - - + -
240A PHE* 4.1 26.5 - - + -
241A LEU* 5.3 4.7 - - + -
244A ILE* 5.7 0.9 - - + -
100B PHE* 3.5 38.4 - - + -
103B VAL* 4.4 21.1 - - + -
104B PHE* 3.8 26.0 - - + -
107B LEU* 4.3 14.1 - - + -
204B GLN 2.9 18.8 + - - +
205B ILE* 3.4 11.2 - - + +
206B LEU 3.1 0.2 - - - -
207B ARG* 1.3 76.3 - - - +
209B ILE* 1.3 66.4 + - + +
211B MET* 3.2 22.8 + - + +
212B ASP 4.7 0.2 + - - -
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Residues in contact with ILE 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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237A TYR* 3.8 19.5 + - - +
241A LEU* 4.0 30.3 - - + -
168B PHE* 5.6 0.3 - - - -
205B ILE* 3.0 22.4 + - + +
206B LEU* 3.5 9.9 - - - +
208B MET* 1.3 75.0 - - - +
210B ARG* 1.3 62.9 + - - +
211B MET 3.0 1.6 + - - -
212B ASP* 3.2 19.0 + - + +
213B ARG 4.7 0.2 + - - -
218B TRP* 5.7 6.1 - - + +
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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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99B VAL* 6.3 0.4 - - - +
137B PHE* 5.4 10.7 - - - -
140B GLU* 2.7 36.3 + - - -
141B TYR* 5.9 2.2 - - - +
144B ARG* 3.0 17.9 - - - +
168B PHE* 3.0 47.7 - - + -
171B ILE* 6.0 3.6 - - + -
172B ASP* 2.6 39.2 + - - +
206B LEU* 2.9 13.6 + - + +
207B ARG* 3.2 25.1 - - - +
208B MET 3.1 0.2 - - - -
209B ILE* 1.3 77.4 - - - +
211B MET* 1.3 73.4 + - - +
212B ASP 3.0 1.6 + - - -
213B ARG* 3.4 17.4 + - - +
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Residues in contact with MET 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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237A TYR* 6.5 0.4 - - + -
96B HIS* 3.5 51.8 - - + +
99B VAL* 4.3 11.2 - - + -
100B PHE* 3.9 31.6 - - + -
103B VAL* 6.1 4.9 - - + -
207B ARG 3.7 4.3 + - - +
208B MET* 3.2 18.2 + - + +
209B ILE 3.0 1.4 + - - -
210B ARG* 1.3 91.0 - - - +
212B ASP* 1.3 64.7 + - - +
213B ARG* 3.7 10.9 - - - +
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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