Contacts of the helix formed by residues 197 - 215 (chain A) in PDB entry 1CJY
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 GLY 197 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A GLY* 1.3 73.8 - - - -
198A GLY* 1.3 69.4 + - - +
200A ARG* 3.3 29.5 + - - +
201A ALA* 3.0 16.9 + - - +
228A SER* 4.1 4.4 + - - -
229A GLY 3.9 3.2 - - - +
555A ASN* 3.8 5.3 + - - +
680A THR* 4.1 14.7 - - - +
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Residues in contact with GLY 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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197A GLY* 1.3 79.0 - - - +
199A PHE* 1.3 58.0 + - - -
201A ALA* 3.1 2.6 + - - +
202A MET* 3.0 20.3 + - - +
229A GLY* 3.7 9.9 - - - -
232A TRP* 3.9 17.0 - - - -
397A PHE* 3.4 35.5 - - - -
680A THR 4.4 4.3 - - - -
683A PHE* 5.4 0.2 - - - -
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Residues in contact with PHE 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A GLY* 1.3 69.6 - - - -
200A ARG* 1.3 57.6 + - - +
202A MET* 3.5 26.0 - - + -
203A VAL* 2.8 37.8 + - + +
232A TRP* 3.7 28.3 - + - -
259A VAL* 3.6 28.0 - - + -
263A PRO* 4.3 9.0 - - + -
299A ILE* 4.6 7.2 - - + -
302A THR* 4.1 19.5 - - + -
303A LEU* 4.3 4.0 - - + -
680A THR 4.8 1.0 + - - -
682A ASN 4.0 9.4 + - - +
683A PHE* 3.1 55.5 - + + -
685A TYR* 3.7 19.1 - + + -
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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
----------------------------------------------------------
197A GLY* 3.3 16.5 + - - +
198A GLY 3.1 0.6 - - - -
199A PHE* 1.3 76.6 - - - +
201A ALA* 1.3 58.1 + - - +
204A GLY* 2.9 28.1 + - - -
418A GLU* 4.2 1.0 + - - -
576A PHE* 2.9 30.5 + - - +
577A SER* 4.3 0.4 - - - +
578A ALA* 3.4 17.2 - - - +
642A LEU* 3.5 24.5 - - + +
670A ILE* 4.6 0.4 - - - -
671A PHE* 4.1 18.8 - - - -
678A PHE* 2.6 44.1 + - + +
679A SER* 3.9 2.1 + - - +
680A THR* 3.1 38.0 + - - +
682A ASN 5.5 0.2 + - - -
685A TYR* 3.3 19.0 + - - +
693A LEU* 3.4 23.2 - - + +
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Residues in contact with ALA 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A SER 3.3 15.5 - - - +
196A GLY 3.3 33.9 - - - +
197A GLY* 3.0 7.6 + - - +
198A GLY 3.4 8.5 - - - +
200A ARG* 1.3 78.8 - - - +
202A MET* 1.3 57.0 + - - +
205A PHE* 2.9 32.7 + - - +
229A GLY* 4.0 7.2 - - - -
230A SER* 4.1 0.9 + - - +
576A PHE* 3.8 17.5 - - + +
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Residues in contact with MET 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 GLY 3.0 13.0 + - - +
199A PHE* 3.6 35.2 - - + +
200A ARG 3.2 0.2 - - - -
201A ALA* 1.3 74.3 - - - +
203A VAL* 1.3 72.8 + - + +
205A PHE* 4.0 0.9 - - - -
206A SER* 3.2 21.3 + - - -
229A GLY 3.7 12.5 + - - +
232A TRP* 4.0 8.3 - - + +
233A TYR* 3.9 29.6 - - + +
236A THR* 5.5 0.2 - - - -
255A LEU* 3.7 20.4 - - + -
259A VAL* 3.7 28.3 - - + -
303A LEU* 3.8 31.2 - - + -
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Residues in contact with VAL 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 PHE* 2.8 23.5 + - + +
202A MET* 1.3 82.9 - - + +
204A GLY* 1.3 65.6 + - - +
206A SER* 2.8 23.2 + - - -
207A GLY 3.4 2.8 + - - -
255A LEU* 4.9 0.7 - - - -
259A VAL* 5.2 2.0 - - + -
685A TYR* 4.0 17.3 - - + -
690A PHE* 3.5 65.1 - - + +
693A LEU* 4.1 12.6 - - + -
694A HIS* 4.0 12.3 - - + +
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Residues in contact with GLY 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 ARG 2.9 17.5 + - - -
203A VAL* 1.3 77.5 - - - +
205A PHE* 1.3 62.1 + - - +
207A GLY* 2.9 13.2 + - - -
208A VAL* 3.1 8.7 + - - +
576A PHE* 3.6 19.1 - - - -
693A LEU* 4.0 11.3 - - - +
697A MET* 3.5 19.2 - - - +
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Residues in contact with PHE 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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192A ILE* 3.8 30.1 - - + -
193A LEU 4.0 3.1 - - - -
194A GLY* 3.6 26.9 - - - -
201A ALA 2.9 20.3 + - - +
202A MET 4.0 2.9 - - - +
204A GLY* 1.3 74.4 - - - +
206A SER* 1.3 57.4 + - - +
208A VAL* 3.3 18.5 + - + +
209A MET* 2.9 45.4 + - + +
224A VAL* 4.3 7.2 - - + -
225A ALA 4.7 0.9 - - - -
230A SER* 4.0 28.9 - - - +
233A TYR* 4.1 13.5 - + + -
234A MET* 4.0 22.2 - - + -
574A PHE* 4.6 1.6 - + + -
576A PHE* 3.3 15.2 - + + -
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Residues in contact with SER 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 MET 3.2 9.4 + - - -
203A VAL* 2.8 21.4 + - - -
204A GLY 3.1 1.0 + - - -
205A PHE* 1.3 76.2 - - - +
207A GLY* 1.3 62.2 + - - +
209A MET* 3.4 2.1 + - - +
210A LYS 3.0 14.6 + - - -
233A TYR* 3.2 40.5 + - - -
252A ASN* 3.0 24.8 + - - -
255A LEU* 4.1 4.9 - - - -
690A PHE* 4.2 6.8 - - - -
694A HIS* 3.1 12.3 + - - -
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Residues in contact with GLY 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A VAL 3.4 1.4 + - - -
204A GLY 2.9 7.0 + - - -
206A SER* 1.3 80.5 + - - +
208A VAL* 1.3 63.1 + - - +
210A LYS* 3.2 4.2 + - - +
211A ALA 3.1 17.7 + - - -
694A HIS* 3.3 39.3 - - - -
698A HIS* 3.6 17.3 - - - -
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Residues in contact with VAL 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A GLY 3.1 12.7 + - - +
205A PHE* 3.4 18.4 - - + +
207A GLY* 1.3 76.7 - - - +
209A MET* 1.3 57.3 + - - +
211A ALA* 3.2 3.7 + - - +
212A LEU* 2.8 38.9 + - + +
574A PHE* 3.4 52.7 - - + -
576A PHE* 4.0 8.1 - - + -
697A MET* 3.7 21.9 - - + +
701A THR* 3.7 12.1 - - - +
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Residues in contact with MET 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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192A ILE* 4.6 2.9 - - - -
205A PHE* 2.9 48.3 + - + +
206A SER 3.9 1.6 - - - +
208A VAL* 1.3 72.2 - - - +
210A LYS* 1.3 66.9 + - - +
212A LEU* 4.1 12.1 - - - +
213A TYR* 2.9 26.5 + - - +
218A LEU* 3.7 39.7 - - + +
224A VAL* 4.3 18.8 - - + -
233A TYR* 3.7 24.7 - - + -
234A MET* 6.1 0.9 - - + -
237A LEU* 3.9 18.2 - - + -
238A TYR* 5.0 6.3 - - + +
243A PHE* 6.0 0.4 - - + -
248A PRO* 3.6 9.5 - - + +
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Residues in contact with LYS 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 SER 3.0 14.6 + - - +
207A GLY 3.2 8.9 + - - +
209A MET* 1.3 77.4 - - - +
211A ALA* 1.3 63.1 + - - +
213A TYR* 3.4 1.0 - - - +
214A GLU* 2.9 63.0 + - + +
248A PRO* 3.5 20.3 - - + +
249A GLU* 3.0 30.8 + - - +
252A ASN* 4.0 4.7 - - + +
694A HIS* 3.8 24.0 + - + +
698A HIS* 4.1 16.1 + - + +
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Residues in contact with ALA 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 GLY 3.1 8.3 + - - +
208A VAL 3.5 7.9 - - - +
210A LYS* 1.3 75.6 - - - +
212A LEU* 1.3 65.4 + - - +
214A GLU* 4.3 1.3 - - - +
215A SER* 2.9 28.9 + - - -
698A HIS* 3.6 24.0 + - - +
701A THR* 3.6 27.8 - - + -
702A LEU* 3.6 18.4 - - + +
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Residues in contact with LEU 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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192A ILE* 3.7 36.3 - - + -
208A VAL* 2.8 41.4 + - + +
209A MET* 4.1 11.2 - - - +
211A ALA* 1.3 73.5 - - - +
213A TYR* 1.3 59.4 + - - +
215A SER* 3.4 4.7 + - - +
217A ILE* 3.0 42.0 + - + -
218A LEU* 2.8 36.6 + - + -
572A ILE* 5.3 2.0 - - + -
574A PHE* 4.3 10.8 - - + -
701A THR* 3.8 18.6 - - + -
708A ILE* 4.8 6.1 - - + -
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Residues in contact with TYR 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 MET 2.9 19.7 + - - +
210A LYS 3.4 3.6 - - - +
211A ALA 3.1 0.2 - - - -
212A LEU* 1.3 77.0 - - - +
214A GLU* 1.3 79.8 + - + +
216A GLY* 3.1 13.9 + - - -
218A LEU* 3.9 24.5 - - + -
219A ASP* 4.6 5.9 - - - +
243A PHE* 4.8 9.6 - + - -
244A PRO* 3.2 27.0 + - + -
245A GLU 3.8 8.8 + - - -
247A GLY* 3.8 18.7 + - - -
248A PRO* 3.5 25.4 - - + -
249A GLU* 5.8 6.3 - - + -
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Residues in contact with GLU 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 LYS* 2.9 46.4 + - + +
211A ALA* 4.3 1.4 - - - +
213A TYR* 1.3 87.4 - - + +
215A SER* 1.3 59.8 + - - +
216A GLY 3.2 1.6 + - - -
249A GLU* 3.5 21.1 - - + +
698A HIS* 3.4 24.6 - - - -
702A LEU* 5.0 4.5 - - + +
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Residues in contact with SER 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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172A LEU* 3.3 22.0 - - - +
211A ALA 2.9 22.0 + - - -
212A LEU* 3.4 1.2 + - - -
214A GLU* 1.3 76.6 - - - +
216A GLY* 1.3 56.3 + - - +
217A ILE* 2.9 32.5 + - - +
702A LEU* 4.3 15.5 - - - -
705A ILE* 5.7 7.6 - - - -
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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