Contacts of the helix formed by residues 197 - 210 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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195A ILE* 3.6 6.1 - - - +
196A PRO* 1.3 81.2 - - - +
198A SER* 1.3 61.6 + - - +
199A ARG* 3.2 19.9 + - - +
200A ARG* 4.0 14.8 - - - -
201A ARG* 3.1 26.8 + - - +
602A TYR* 3.4 24.0 - - - -
603A PRO* 4.4 13.7 - - - +
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Residues in contact with SER 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A PRO 3.7 1.0 + - - -
197A SER* 1.3 70.1 + - - +
199A ARG* 1.3 59.8 + - - +
201A ARG* 3.1 32.9 - - - +
202A ALA* 3.0 22.5 + - - +
314A VAL* 5.4 0.5 - - - +
317A GLU* 3.1 32.8 + - - +
552A GLN* 3.5 13.3 - - - +
553A ASP* 3.1 25.6 + - - +
602A TYR* 3.1 9.1 + - - -
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Residues in contact with ARG 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197A SER* 3.2 11.4 + - - +
198A SER* 1.3 77.4 + - - +
200A ARG* 1.3 65.5 + - - +
202A ALA* 3.2 6.3 + - - +
203A ALA* 3.0 22.0 + - + +
317A GLU* 3.2 15.9 + - - +
318A GLN* 5.4 0.5 - - - +
553A ASP* 3.1 37.9 + - + -
602A TYR* 5.1 2.3 - - + -
457B ASP* 5.4 1.4 - - - +
460B ASP* 3.0 41.5 + - - -
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Residues in contact with ARG 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A ILE* 3.6 23.0 - - + +
197A SER* 3.5 19.7 + - - +
198A SER 3.4 0.2 - - - -
199A ARG* 1.3 79.9 - - - +
201A ARG* 1.3 57.1 + - - +
203A ALA* 3.3 21.2 + - - +
204A ARG* 2.9 55.3 + - - +
207A GLU* 3.8 18.8 + - - -
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Residues in contact with ARG 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A LEU* 3.1 65.9 - - + +
195A ILE* 2.8 36.9 + - + +
196A PRO 3.0 13.3 + - - -
197A SER 3.1 11.5 + - - +
198A SER* 3.1 34.7 - - - +
200A ARG* 1.3 75.1 - - - +
202A ALA* 1.3 64.5 + - - +
204A ARG 3.5 0.3 + - - -
205A LEU* 3.2 21.3 + - - +
314A VAL* 3.7 10.5 - - + +
513A VAL 4.8 2.4 + - - -
515A THR* 3.6 17.9 + - - +
518A GLU* 2.6 36.1 + - - -
552A GLN* 3.6 10.5 + - - +
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Residues in contact with ALA 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A SER 3.0 14.0 + - - +
199A ARG* 3.2 9.4 + - - +
201A ARG* 1.3 75.8 - - - +
203A ALA* 1.3 63.9 + - - +
205A LEU* 3.3 3.6 + - - +
206A PHE 3.1 18.2 + - - -
314A VAL* 3.3 31.8 - - + +
315A LEU* 4.4 1.0 - - - +
317A GLU* 3.8 7.0 - - + +
318A GLN* 3.5 34.3 - - + +
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Residues in contact with ALA 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A ARG* 3.0 13.1 + - + +
200A ARG* 3.4 26.0 - - - +
202A ALA* 1.3 77.5 - - - +
204A ARG* 1.3 56.6 + - - +
206A PHE* 3.5 4.3 + - - +
207A GLU* 3.0 27.7 + - - +
215A PRO* 5.0 3.5 - - - +
318A GLN* 4.3 8.9 - - + +
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Residues in contact with ARG 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188A VAL* 4.1 15.2 - - + +
191A GLU* 2.5 36.9 + - - +
192A LEU* 4.0 16.2 - - + -
195A ILE* 4.1 9.2 - - + -
200A ARG* 2.9 40.7 + - - +
201A ARG 3.8 4.9 - - - +
203A ALA* 1.3 74.7 - - - +
205A LEU* 1.3 61.3 + - - +
207A GLU* 3.2 25.2 + - - +
208A TRP* 2.9 51.8 + - - +
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Residues in contact with LEU 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188A VAL* 4.0 27.4 - - + -
189A LEU* 4.8 6.1 - - + -
192A LEU* 4.2 18.2 - - + -
201A ARG 3.2 14.8 + - - +
202A ALA 3.3 3.3 + - - +
204A ARG* 1.3 77.9 - - - +
206A PHE* 1.3 61.3 + - - +
208A TRP* 3.2 8.8 + - + +
209A LEU* 2.9 27.9 + - - +
310A GLN 5.5 0.2 - - - -
311A PHE* 3.8 48.5 - - + +
314A VAL* 3.7 29.6 - - + -
315A LEU* 4.0 8.7 - - + -
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Residues in contact with PHE 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A ALA 3.1 10.9 + - - +
203A ALA* 3.9 4.7 - - - +
205A LEU* 1.3 76.5 - - - +
207A GLU* 1.3 65.0 + - - +
209A LEU* 3.2 23.1 + - + +
210A ILE* 3.2 47.3 + - + +
215A PRO* 4.1 11.7 - - + -
218A PHE* 3.5 26.5 - + - -
219A TYR* 3.4 34.5 - + - -
315A LEU* 3.8 7.5 - - + +
318A GLN* 3.3 40.2 - - + +
319A PHE* 4.0 7.0 - + - -
347A PHE* 3.9 19.1 - + - -
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Residues in contact with GLU 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200A ARG* 3.8 26.8 + - - -
203A ALA 3.0 13.4 + - - +
204A ARG* 3.3 29.9 + - - +
206A PHE* 1.3 77.4 - - - +
208A TRP* 1.3 59.2 + - - +
210A ILE* 4.0 2.6 - - - +
211A ALA* 3.2 24.5 + - + +
213A MET 4.6 1.2 - - - +
215A PRO* 3.7 30.7 - - + +
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Residues in contact with TRP 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A PRO* 3.5 17.7 + - + +
185A LEU* 3.4 39.0 - - + -
188A VAL* 3.7 27.8 - - + -
204A ARG* 2.9 30.7 + - - +
205A LEU* 3.4 20.0 - - + +
207A GLU* 1.3 75.6 - - - +
209A LEU* 1.3 82.3 + - - +
210A ILE 3.2 0.7 + - - -
211A ALA* 3.3 8.7 + - + -
232A ARG* 3.4 1.7 + - - -
237A TYR* 2.7 87.7 + + - -
238A TYR* 4.0 13.5 - + - -
311A PHE* 4.0 16.2 - + - -
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Residues in contact with LEU 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A LEU 2.9 18.6 + - - +
206A PHE* 3.2 25.7 + - + +
208A TRP* 1.3 82.1 - - + +
210A ILE* 1.3 57.5 + - + +
232A ARG* 2.7 27.1 + - - +
238A TYR* 4.4 7.6 - - + -
311A PHE* 3.9 13.0 - - + -
315A LEU* 4.2 11.4 - - + -
347A PHE* 4.6 6.7 - - + -
349A LEU* 3.8 26.5 - - + -
396A LEU* 3.5 26.4 - - + +
420A LEU* 3.7 27.1 - - + -
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Residues in contact with ILE 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A PHE* 3.2 53.6 + - + +
207A GLU* 4.1 3.4 - - - +
208A TRP 3.2 0.4 - - - -
209A LEU* 1.3 84.4 - - + +
211A ALA* 1.3 67.8 + - - +
213A MET* 3.1 45.8 + - + +
214A PRO 4.1 0.2 - - - -
215A PRO* 3.7 17.7 - - + -
218A PHE* 3.7 21.8 - - + -
230A VAL* 4.2 8.5 - - + +
232A ARG* 3.6 1.6 - - - +
347A PHE* 4.4 9.0 - - + -
396A LEU* 4.2 20.2 - - + -
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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