Contacts of the helix formed by residues 196 - 209 (chain D) in PDB entry 1CX2
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 MET 196 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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195D ASN* 1.3 73.9 - - - +
197D MET* 1.3 59.0 + - - +
198D PHE 3.3 0.4 - - - -
199D ALA* 3.7 17.5 - - + -
200D PHE* 3.0 63.4 + - + +
391D LEU* 4.9 2.2 - - + -
392D PRO* 3.5 39.3 - - + -
395D PHE* 3.7 13.9 - - + -
426D PHE* 3.0 35.2 + - + -
429D GLN* 3.4 33.5 + - + +
431D ALA* 4.4 10.3 - - - -
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Residues in contact with MET 197 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195D ASN* 3.5 5.6 - - - +
196D MET* 1.3 74.3 - - - +
198D PHE* 1.3 67.5 + - - +
201D PHE* 3.1 12.6 + - - +
300D MET* 3.6 20.6 - - + +
301D TYR* 2.9 34.6 + - - +
423D VAL* 3.2 48.9 - - + +
426D PHE* 3.5 23.7 - - + +
564D ILE* 4.9 2.9 - - + -
568D ILE* 4.3 9.2 - - + -
578D THR* 3.3 21.8 - - + -
579D SER 3.2 17.7 - - - +
580D PHE* 4.0 4.3 - - + -
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Residues in contact with PHE 198 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194D SER* 4.3 12.8 - - - -
195D ASN* 2.8 22.0 + - - +
197D MET* 1.3 75.0 - - - +
199D ALA* 1.3 73.5 + - + +
201D PHE* 2.8 12.5 + - - +
202D ALA* 2.9 27.5 + - + -
348D TYR* 4.0 27.4 - + - -
351D HIS* 3.3 25.6 - + - -
352D LEU* 3.1 33.9 - - + -
387D TRP* 4.7 0.9 - + - -
390D LEU* 4.5 18.6 - - + -
517D ILE* 5.5 0.7 - - + -
580D PHE* 3.3 46.6 - + + +
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Residues in contact with ALA 199 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195D ASN 3.1 16.8 + - - +
196D MET* 3.9 25.1 - - + +
197D MET 3.4 0.4 - - - -
198D PHE* 1.3 89.6 - - + +
200D PHE* 1.3 62.1 + - + +
202D ALA* 3.5 4.0 + - - +
203D GLN 3.3 6.9 + - - -
390D LEU* 4.5 17.7 - - + +
391D LEU* 6.1 2.2 - - + -
431D ALA* 4.3 10.1 - - + -
682D HEM 3.3 25.4 - - + +
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Residues in contact with PHE 200 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196D MET* 3.0 43.3 + - + +
199D ALA* 1.3 75.8 - - + +
201D PHE* 1.3 59.2 + - - +
203D GLN* 3.2 30.3 + - + +
204D HIS* 2.9 30.7 + - - +
295D VAL* 3.6 17.0 - - + -
297D GLY* 3.8 19.5 - - - -
298D LEU* 4.1 2.1 - - - +
300D MET* 6.0 0.9 - - - -
301D TYR* 3.7 14.9 - - + -
391D LEU* 5.1 2.7 - - + -
395D PHE* 4.3 7.9 - + - -
407D PHE* 3.6 22.7 - + - -
426D PHE* 3.3 40.2 - + + -
682D HEM 4.0 12.3 - - + -
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Residues in contact with PHE 201 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197D MET 3.1 17.5 + - - +
198D PHE* 2.8 5.3 + - - +
200D PHE* 1.3 74.0 - - - +
202D ALA* 1.3 59.3 + - - +
203D GLN 2.9 4.3 + - - -
204D HIS* 3.1 3.7 + + - -
205D PHE* 2.8 46.9 + + + +
301D TYR* 3.0 39.7 - + + -
305D TRP* 4.2 28.0 - + - -
340D THR* 5.5 2.2 - - + -
343D ILE* 3.7 20.9 - - + -
344D VAL* 3.6 27.6 - - + -
348D TYR* 3.8 17.5 - + + -
564D ILE* 3.9 12.3 - - + -
567D LEU* 4.7 1.8 - - + -
580D PHE* 3.5 20.6 - + + -
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Residues in contact with ALA 202 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198D PHE* 2.9 25.6 + - + +
199D ALA* 3.8 2.7 - - - +
201D PHE* 1.3 76.3 - - - +
203D GLN* 1.3 51.8 + - - +
205D PHE* 4.4 2.2 - - - -
206D THR* 2.5 35.2 + - - +
348D TYR* 3.0 38.7 - - + +
387D TRP* 4.5 2.2 - - + -
682D HEM 3.5 23.4 - - + +
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Residues in contact with GLN 203 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199D ALA 3.3 3.3 + - - +
200D PHE* 3.2 33.5 + - - +
201D PHE 2.9 0.6 - - - -
202D ALA* 1.3 78.5 - - - +
204D HIS* 1.3 62.4 + - - +
206D THR* 3.3 0.3 + - - -
207D HIS* 2.6 47.3 + - + +
295D VAL* 4.6 2.2 - - - +
298D LEU* 2.9 39.9 - - + +
682D HEM 3.0 65.8 + - + +
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Residues in contact with HIS 204 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200D PHE 2.9 16.5 + - - +
201D PHE* 3.8 6.5 - + - +
203D GLN* 1.3 76.3 - - - +
205D PHE* 1.3 69.6 + - + +
207D HIS* 3.3 7.3 + - - +
232D HIS* 3.6 27.7 - - - -
233D ILE* 5.1 1.6 - - + -
292D PHE* 3.0 50.5 - + - -
298D LEU* 3.8 17.7 + - + +
301D TYR* 3.8 21.3 - + + +
302D ALA* 4.0 20.1 + - + -
305D TRP* 3.0 42.0 + + - -
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Residues in contact with PHE 205 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201D PHE* 2.8 34.0 + + + +
202D ALA* 4.6 0.4 - - - -
204D HIS* 1.3 76.0 - - + +
206D THR* 1.3 81.0 + - + +
207D HIS 3.0 5.5 + - - -
208D GLN* 3.3 40.0 + - - +
209D PHE* 3.6 22.6 - + - -
228D VAL* 4.3 4.7 - - + -
232D HIS* 4.6 4.7 - - - -
340D THR* 3.8 22.0 - - + -
341D ILE* 6.3 0.2 - - - -
344D VAL* 3.3 51.1 - - + -
348D TYR* 4.5 15.3 - + - -
385D TYR* 5.1 2.7 - - - -
530D SER* 5.3 4.0 - - - -
534D LEU* 4.2 13.0 - - + -
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Residues in contact with THR 206 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202D ALA 2.5 22.2 + - - +
203D GLN* 3.3 6.9 + - - -
205D PHE* 1.3 91.9 - - + +
207D HIS* 1.3 64.2 + - - +
208D GLN 3.1 1.8 + - - -
209D PHE* 3.3 15.6 + - + -
210D PHE* 2.8 53.6 + - + -
348D TYR* 4.2 0.4 - - - +
385D TYR* 3.0 43.1 - - + +
682D HEM 4.4 2.1 - - - +
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Residues in contact with HIS 207 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203D GLN* 2.6 45.9 + - + +
204D HIS 3.6 4.5 - - - +
205D PHE 3.0 2.8 - - - -
206D THR* 1.3 83.7 + - - +
208D GLN* 1.3 58.1 - - - +
210D PHE* 3.1 14.0 - - + +
211D LYS* 3.6 0.5 - - - +
289D GLN* 2.7 32.7 + - - +
291D VAL* 4.6 14.8 - - + -
292D PHE* 3.4 28.3 - + + -
298D LEU* 5.5 1.6 - - + -
682D HEM 3.7 60.9 + + + +
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Residues in contact with GLN 208 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204D HIS 4.0 1.0 + - - -
205D PHE* 3.3 12.6 + - - +
206D THR 3.1 0.8 - - - -
207D HIS* 1.3 78.0 - - - +
209D PHE* 1.3 92.2 + - + +
211D LYS* 3.1 15.1 - - - +
223D GLY* 4.1 4.0 - - - -
227D GLY 4.1 5.4 - - - +
228D VAL* 3.1 39.0 - - - +
229D ASP* 4.3 1.3 - - - +
230D LEU* 3.0 26.9 - - - +
231D ASN* 3.1 32.0 + - - +
232D HIS* 2.7 40.8 + - + +
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Residues in contact with PHE 209 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148D TYR* 4.5 0.2 - - - -
205D PHE* 3.6 35.4 - + - -
206D THR* 3.7 30.1 - - + -
208D GLN* 1.3 109.6 - - + +
210D PHE* 1.3 79.8 + + - +
211D LYS* 3.4 3.8 + - - +
221D THR* 3.9 6.9 + - - -
223D GLY* 4.4 4.9 - - - -
227D GLY* 4.0 20.9 - - - +
228D VAL* 4.0 14.1 - - + -
377D ILE* 2.8 47.3 - - + +
381D PHE* 4.0 18.6 - + - -
530D SER* 5.9 1.3 - - - -
534D LEU* 5.5 2.9 - - + -
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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