Contacts of the helix formed by residues 197 - 216 (chain A) in PDB entry 3CRK
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 VAL 197 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195A CYS* 3.2 3.3 + - - +
196A SER* 1.3 69.0 - - - +
198A SER* 1.3 59.4 + - - +
200A VAL* 3.2 6.1 + - - +
201A VAL* 3.0 28.5 + - + +
226A GLU* 4.9 0.4 - - - +
236A ILE* 3.5 17.4 + - + +
238A MET* 4.1 20.4 - - + -
245A LEU* 4.5 13.4 - - + +
277A VAL* 3.6 33.4 - - + -
284A LEU* 3.9 30.5 - - + -
286A ILE* 3.8 23.3 - - + -
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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
----------------------------------------------------------
196A SER* 3.3 5.1 + - - -
197A VAL* 1.3 78.9 - - - +
199A ASP* 1.3 57.6 + - - +
201A VAL* 3.4 9.2 - - - +
202A LYS* 2.8 41.7 + - - +
224A ILE* 3.6 25.6 - - - +
226A GLU* 2.6 31.4 + - - +
236A ILE 4.8 0.6 + - - -
277A VAL* 4.4 2.3 - - - +
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Residues in contact with ASP 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A SER* 3.1 31.4 + - - +
198A SER* 1.3 77.3 - - - +
200A VAL* 1.3 59.1 + - + +
202A LYS* 3.3 19.1 + - - +
203A ASP* 2.9 38.9 + - - +
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Residues in contact with VAL 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A CYS* 3.7 24.0 - - - -
196A SER 3.5 13.0 - - - +
197A VAL 3.2 7.0 + - - +
199A ASP* 1.3 74.9 - - + +
201A VAL* 1.3 60.0 + - - +
203A ASP* 3.3 7.2 + - - +
204A ALA* 3.0 29.1 + - - +
242A PRO* 4.0 13.5 - - + +
245A LEU* 3.9 17.0 - - + -
246A TYR* 3.6 40.2 - - + +
249A LEU* 4.1 2.5 - - + -
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Residues in contact with VAL 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A VAL* 3.0 29.9 + - + +
198A SER* 3.4 11.4 - - - +
200A VAL* 1.3 76.2 - - - +
202A LYS* 1.3 57.0 + - - +
204A ALA* 4.7 0.2 - - - -
205A TYR* 3.0 24.8 + - - +
222A LEU* 4.5 1.6 - - + -
224A ILE* 3.9 18.8 - - + -
249A LEU* 3.7 28.9 - - + -
253A PHE* 3.3 16.4 - - + -
275A ILE* 3.9 37.9 - - + -
277A VAL* 4.7 1.6 - - + -
286A ILE* 4.5 3.4 - - + -
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Residues in contact with LYS 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A SER* 2.8 30.9 + - - +
199A ASP* 3.6 16.9 + - - +
201A VAL* 1.3 73.7 - - - +
203A ASP* 1.3 59.8 + - - +
205A TYR* 3.6 4.9 - - - +
206A ASP* 2.9 42.8 + - - +
222A LEU* 4.5 7.9 - - + -
224A ILE* 3.8 24.9 - - + -
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Residues in contact with ASP 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A ASP* 2.9 24.7 + - - +
200A VAL* 3.7 7.2 - - - +
202A LYS* 1.3 76.2 - - - +
204A ALA* 1.3 65.6 + - - +
206A ASP* 3.3 10.2 + - - +
207A MET* 3.1 29.4 + - + +
246A TYR* 3.8 15.0 - - + -
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Residues in contact with ALA 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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200A VAL 3.0 16.8 + - - +
201A VAL 3.9 1.3 - - - +
203A ASP* 1.3 75.8 - - - +
205A TYR* 1.3 62.5 + - - +
208A ALA* 3.1 24.8 + - - +
246A TYR* 3.5 19.9 - - + +
249A LEU* 3.7 15.7 - - + -
250A PHE* 3.6 32.1 - - - +
253A PHE* 3.8 7.5 - - + -
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Residues in contact with TYR 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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201A VAL 3.0 19.4 + - - +
202A LYS 3.6 2.9 - - - +
204A ALA* 1.3 73.8 - - - +
206A ASP* 1.3 69.2 + - - +
208A ALA* 3.2 1.0 + - - -
209A LYS* 2.6 75.8 + - + +
220A PRO 2.6 26.7 + - - -
221A ASP* 3.3 10.7 - - - -
222A LEU* 3.5 42.7 + - + -
253A PHE* 3.4 29.7 - + + -
257A MET* 3.4 26.1 - - + +
273A ILE* 4.8 2.9 - - + -
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Residues in contact with ASP 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A LYS* 2.9 35.9 + - - +
203A ASP* 3.7 10.6 - - - +
205A TYR* 1.3 89.2 - - - +
207A MET* 1.3 62.2 + - + +
209A LYS* 3.7 8.9 - - - +
210A LEU* 3.0 29.3 + - - +
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Residues in contact with MET 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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203A ASP* 3.1 16.8 + - + +
204A ALA 3.9 0.7 - - - +
206A ASP* 1.3 78.1 - - + +
208A ALA* 1.3 63.9 - - - +
210A LEU* 3.4 27.2 - - + +
211A LEU* 3.2 30.7 + - + +
246A TYR* 3.1 29.6 - - + +
250A PHE* 3.8 13.0 - - + -
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Residues in contact with ALA 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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204A ALA 3.1 18.8 + - - +
205A TYR 3.7 1.8 - - - +
207A MET* 1.3 72.7 - - - +
209A LYS* 1.3 61.0 + - - +
211A LEU* 3.1 4.6 + - - +
212A CYS* 2.9 30.3 + - - +
250A PHE* 3.6 10.2 - - + -
253A PHE* 3.7 24.0 - - + -
254A LYS* 3.9 21.7 - - + +
257A MET* 3.6 11.6 - - - +
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Residues in contact with LYS 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A TYR* 2.6 61.4 + - + +
206A ASP* 3.7 8.5 - - - +
208A ALA* 1.3 72.2 - - - +
210A LEU* 1.3 54.9 + - - +
212A CYS* 3.2 1.9 + - - +
213A ASP* 2.8 43.1 + - + +
219A SER* 3.4 28.4 + - - +
220A PRO 3.7 3.2 + - - +
221A ASP* 3.8 13.7 + - - -
257A MET* 3.5 16.2 - - + +
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Residues in contact with LEU 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 ASP 3.0 17.5 + - - +
207A MET* 3.4 30.7 - - + +
209A LYS* 1.3 79.0 - - - +
211A LEU* 1.3 62.2 + - + +
213A ASP* 4.1 3.6 - - + +
214A LYS* 2.9 46.3 + - + +
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Residues in contact with LEU 211 (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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207A MET* 3.2 16.2 + - + +
208A ALA* 3.1 7.4 + - - +
210A LEU* 1.3 79.7 - - + +
212A CYS* 1.3 61.9 + - - +
214A LYS* 3.5 4.3 + - - +
215A TYR* 3.0 31.8 + - - +
250A PHE* 3.6 31.0 - - + -
254A LYS* 4.3 15.5 - - + +
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Residues in contact with CYS 212 (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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208A ALA 2.9 15.8 + - - +
209A LYS 3.5 4.3 - - - +
211A LEU* 1.3 73.5 - - - +
213A ASP* 1.3 54.2 - - - +
214A LYS 3.0 5.2 + - - -
215A TYR* 4.8 0.7 - - - -
216A TYR* 2.8 53.4 + - + +
218A ALA 3.1 25.1 - - - -
219A SER* 4.0 8.1 - - - -
257A MET* 3.8 28.9 - - + -
261A VAL* 3.7 20.9 - - - -
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Residues in contact with ASP 213 (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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209A LYS* 2.8 24.5 + - + +
210A LEU* 4.3 5.6 - - + +
211A LEU 3.5 0.2 - - - -
212A CYS* 1.3 71.6 - - - +
214A LYS* 1.3 64.2 + - + +
217A MET* 3.2 27.4 - - - +
218A ALA* 3.5 12.5 - - - +
219A SER* 2.8 33.9 + - - -
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Residues in contact with LYS 214 (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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210A LEU* 2.9 38.7 + - + +
211A LEU* 3.5 4.7 + - - +
212A CYS 3.0 0.8 - - - -
213A ASP* 1.3 88.1 - - + +
215A TYR* 1.3 59.0 + - - +
216A TYR 3.5 1.1 - - - -
217A MET* 3.7 22.0 - - - +
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Residues in contact with TYR 215 (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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211A LEU 3.0 18.7 + - - +
212A CYS* 4.2 1.8 - - - +
214A LYS* 1.3 76.4 - - - +
216A TYR* 1.3 96.8 + + + +
217A MET* 5.3 1.1 - - - -
258A ARG* 6.1 2.9 - - - -
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Residues in contact with TYR 216 (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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212A CYS* 2.8 32.0 + - - +
215A TYR* 1.3 110.2 - + + +
217A MET* 1.3 72.3 + - - +
218A ALA* 3.1 12.3 + - - +
258A ARG* 3.4 34.0 + - + +
261A VAL* 3.6 26.5 - - + -
262A GLU* 3.0 37.7 + - + -
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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
------------------------------------------------------------
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