Contacts of the helix formed by residues 197 - 211 (chain B) in PDB entry 4CCN
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 SER 197 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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195B ILE* 3.8 4.4 - - - +
196B PRO* 1.3 80.4 - - - +
198B SER* 1.3 57.4 + - - +
199B ARG* 3.1 21.7 + - - +
200B ARG* 3.3 20.7 + - - +
201B ARG* 2.9 26.3 + - - +
602B TYR* 3.3 19.7 - - - -
603B PRO* 4.5 15.7 - - - +
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Residues in contact with SER 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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196B PRO 3.5 0.6 + - - -
197B SER* 1.3 71.1 + - - +
199B ARG* 1.3 61.5 + - - +
200B ARG 3.4 0.2 - - - -
201B ARG* 3.3 32.5 - - - +
202B ALA* 3.0 22.3 + - - +
314B VAL* 5.3 0.7 - - - +
317B GLU* 2.8 28.8 + - - +
552B GLN* 3.7 16.1 - - - +
553B ASP* 3.1 28.8 + - - +
602B TYR* 2.9 10.1 + - - -
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Residues in contact with ARG 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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457A ASP* 5.4 2.4 - - - +
460A ASP* 3.0 41.5 + - - -
197B SER* 3.1 11.8 + - - +
198B SER* 1.3 79.9 + - - +
200B ARG* 1.3 63.4 + - - +
202B ALA* 3.5 3.8 + - - +
203B ALA* 3.1 22.3 + - + +
317B GLU* 4.2 13.5 - - + +
318B GLN* 5.5 0.5 - - - +
553B ASP* 2.8 36.9 + - + +
602B TYR* 4.7 1.2 - - + -
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Residues in contact with ARG 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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191B GLU* 5.4 0.2 + - - -
195B ILE* 3.6 26.0 - - + +
197B SER* 3.3 20.1 + - - +
199B ARG* 1.3 77.7 - - - +
201B ARG* 1.3 56.5 + - - +
203B ALA* 3.3 23.0 + - - +
204B ARG* 2.8 64.7 + - - +
207B GLU* 3.9 14.6 + - - -
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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
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192B LEU* 3.0 62.0 - - + +
195B ILE* 3.1 17.5 + - + +
196B PRO 2.7 30.7 + - - -
197B SER 2.9 8.3 + - - +
198B SER* 3.3 30.7 - - - +
199B ARG 3.2 0.2 - - - -
200B ARG* 1.3 76.7 - - - +
202B ALA* 1.3 57.1 + - - +
204B ARG* 3.2 4.8 + - - +
205B LEU* 2.9 26.7 + - - +
314B VAL* 4.0 10.0 - - + +
513B VAL 4.6 4.4 + - - -
515B THR* 3.5 14.7 - - - +
518B GLU* 2.9 26.6 + - - -
552B GLN* 3.3 21.2 - - - +
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Residues in contact with ALA 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B SER 3.0 15.7 + - - +
199B ARG 3.8 4.0 - - - +
200B ARG 3.3 0.2 - - - -
201B ARG* 1.3 74.4 - - - +
203B ALA* 1.3 65.7 + - - +
205B LEU* 3.4 1.9 + - - +
206B PHE 3.1 18.9 + - - -
314B VAL* 3.2 35.4 - - + +
315B LEU* 4.5 1.0 - - - +
317B GLU* 3.8 7.6 - - + -
318B GLN* 3.5 34.4 - - + +
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Residues in contact with ALA 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 ARG* 3.1 19.5 + - + +
200B ARG* 3.6 22.2 + - - +
202B ALA* 1.3 78.0 - - - +
204B ARG* 1.3 61.9 + - - +
206B PHE* 3.6 3.8 + - - +
207B GLU* 3.1 23.2 + - - +
215B PRO* 5.1 2.9 - - - +
318B GLN* 4.4 8.9 - - + +
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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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188B VAL* 4.3 16.4 - - + +
191B GLU* 2.8 40.7 + - - +
192B LEU* 3.8 17.5 - - + -
195B ILE* 4.1 6.3 - - + -
200B ARG* 2.8 45.1 + - - +
201B ARG 3.5 4.7 - - - +
203B ALA* 1.3 76.2 - - - +
205B LEU* 1.3 64.6 + - - +
207B GLU* 3.0 39.4 + - - +
208B TRP* 3.2 33.8 + - - +
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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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188B VAL* 4.5 17.9 - - + -
189B LEU* 5.1 4.5 - - + -
192B LEU* 4.3 16.8 - - + +
201B ARG 2.9 16.7 + - - +
202B ALA 3.9 3.6 - - - +
203B ALA 3.3 0.2 - - - -
204B ARG* 1.3 75.8 - - - +
206B PHE* 1.3 65.9 + - - +
208B TRP* 3.1 19.0 + - + +
209B LEU* 2.9 19.8 + - - +
310B GLN* 6.3 0.2 - - + -
311B PHE* 3.6 56.3 - - + +
314B VAL* 3.8 18.6 - - + -
315B LEU* 3.7 17.3 - - + -
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Residues in contact with PHE 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 ALA 3.1 11.3 + - - +
203B ALA* 4.0 4.3 - - - +
204B ARG 3.4 0.2 - - - -
205B LEU* 1.3 76.6 - - - +
207B GLU* 1.3 63.7 + - - +
209B LEU* 3.1 25.9 + - + +
210B ILE* 3.2 40.6 + - + +
215B PRO* 3.9 15.0 - - + -
218B PHE* 3.5 27.4 - + - -
219B TYR* 3.2 34.5 - + - -
315B LEU* 3.8 8.6 - - + +
318B GLN* 3.4 37.5 - - + +
319B PHE* 4.0 6.1 - + - -
347B PHE* 3.9 22.2 - + - -
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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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200B ARG* 3.9 22.2 + - - -
203B ALA 3.1 16.3 + - - +
204B ARG* 3.0 28.2 + - - +
205B LEU 3.1 0.4 - - - -
206B PHE* 1.3 76.8 - - - +
208B TRP* 1.3 57.3 + - - +
210B ILE* 3.5 2.8 + - - +
211B ALA* 3.0 31.4 + - + +
213B MET 4.7 1.2 - - - +
215B PRO* 3.8 30.1 - - + +
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Residues in contact with TRP 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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184B PRO* 3.4 16.7 + - + +
185B LEU* 3.4 26.9 - - + -
188B VAL* 3.6 31.6 - - + -
204B ARG* 3.2 23.9 + - - +
205B LEU* 3.1 23.1 + - + +
207B GLU* 1.3 78.3 - - - +
209B LEU* 1.3 81.2 + - - +
210B ILE 3.4 0.5 + - - -
211B ALA* 3.4 8.2 + - + -
237B TYR* 2.6 91.9 + + - -
238B TYR* 3.9 15.7 - + - -
311B PHE* 3.8 25.1 - + - -
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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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205B LEU 2.9 13.3 + - - +
206B PHE* 3.1 33.2 + - + +
208B TRP* 1.3 85.4 - - + +
210B ILE* 1.3 57.1 + - + +
232B ARG* 2.9 28.2 + - - +
238B TYR* 4.6 6.7 - - + -
311B PHE* 4.1 21.1 - - + -
315B LEU* 4.2 8.7 - - + -
347B PHE* 4.4 11.2 - - + -
349B LEU* 4.1 15.9 - - + -
396B LEU* 3.4 25.3 - - + +
420B LEU* 3.7 25.6 - - + -
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Residues in contact with ILE 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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206B PHE* 3.2 42.6 + - + +
207B GLU* 3.9 4.0 - - - +
209B LEU* 1.3 77.6 - - + +
211B ALA* 1.3 68.9 + - - +
213B MET* 3.1 45.3 + - + +
215B PRO* 3.6 27.4 - - + -
218B PHE* 3.9 21.5 - - + -
230B VAL* 4.1 10.0 - - + +
232B ARG* 3.8 0.9 - - - -
347B PHE* 4.6 6.5 - - + -
396B LEU* 3.7 24.5 - - + -
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Residues in contact with ALA 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* 3.0 20.3 + - + +
208B TRP* 3.4 5.1 + - - +
209B LEU 3.5 0.2 - - - -
210B ILE* 1.3 78.0 - - - +
212B PRO* 1.3 70.0 - - + +
213B MET 3.6 0.7 - - - +
230B VAL* 3.5 6.6 - - - +
232B ARG* 2.9 24.2 + - - -
237B TYR* 3.6 21.5 - - + +
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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