Contacts of the helix formed by residues 196 - 209 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195C ASN* 1.3 74.8 - - - +
197C MET* 1.3 59.9 + - - +
198C PHE 3.4 0.2 - - - -
199C ALA* 3.7 17.0 - - + -
200C PHE* 3.1 61.9 + - + +
391C LEU* 4.9 2.5 - - + -
392C PRO* 3.5 40.8 - - + -
395C PHE* 3.6 13.0 - - + -
426C PHE* 3.0 34.5 + - + +
429C GLN* 3.3 34.0 + - + +
431C ALA* 4.5 9.2 - - - -
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Residues in contact with MET 197 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195C ASN* 3.6 5.2 - - - +
196C MET* 1.3 74.9 - - - +
198C PHE* 1.3 67.7 + - - +
201C PHE* 3.1 12.8 + - - +
300C MET* 3.6 22.2 - - + +
301C TYR* 2.9 35.8 + - - +
423C VAL* 3.2 47.8 - - + +
426C PHE* 3.6 23.0 - - + +
564C ILE* 5.0 3.4 - - + -
568C ILE* 4.3 8.7 - - + -
578C THR* 3.3 20.6 - - + -
579C SER 3.3 18.6 - - - +
580C PHE* 3.9 4.0 - - + -
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Residues in contact with PHE 198 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194C SER* 4.5 11.2 - - - -
195C ASN* 2.9 21.0 + - - +
197C MET* 1.3 77.1 - - - +
199C ALA* 1.3 70.5 + - + +
201C PHE* 2.9 3.2 + - - +
202C ALA* 2.9 35.7 + - + -
348C TYR* 4.0 26.7 - + - -
351C HIS* 3.3 25.4 - + - -
352C LEU* 3.1 34.3 - - + -
387C TRP* 4.6 0.7 - + - -
390C LEU* 4.6 18.2 - - + -
517C ILE* 5.5 1.1 - - + -
580C PHE* 3.2 46.6 - + + +
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Residues in contact with ALA 199 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195C ASN 3.1 17.5 + - - +
196C MET* 3.9 24.7 - - + +
197C MET 3.3 0.4 - - - -
198C PHE* 1.3 89.6 - - + +
200C PHE* 1.3 61.5 + - + +
202C ALA* 3.5 4.0 + - - +
203C GLN 3.4 7.3 + - - -
390C LEU* 4.6 17.7 - - + +
391C LEU* 6.2 1.6 - - + -
431C ALA* 4.3 10.1 - - + -
682C HEM 3.3 24.5 - - + +
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Residues in contact with PHE 200 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196C MET* 3.1 44.5 + - + +
199C ALA* 1.3 75.8 - - - +
201C PHE* 1.3 60.8 + - - +
203C GLN* 3.2 30.9 + - - +
204C HIS* 3.0 30.1 + - - +
295C VAL* 3.6 16.6 - - + -
297C GLY* 3.8 16.6 - - - -
298C LEU* 4.1 1.9 - - - +
300C MET* 6.0 0.7 - - - -
301C TYR* 3.6 15.2 - - + -
391C LEU* 5.1 2.9 - - + -
395C PHE* 4.3 8.1 - + - -
407C PHE* 3.7 24.9 - + - -
426C PHE* 3.4 39.0 - + + -
682C HEM 4.0 12.1 - - + -
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Residues in contact with PHE 201 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197C MET 3.1 17.2 + - - +
198C PHE* 2.9 4.9 + - - +
200C PHE* 1.3 73.6 - - - +
202C ALA* 1.3 59.5 + - - +
203C GLN 2.9 4.2 + - - -
204C HIS* 3.1 4.1 + + - -
205C PHE* 2.8 46.3 + + + +
301C TYR* 3.1 39.0 - + + -
305C TRP* 4.2 26.2 - + - -
340C THR* 5.5 2.0 - - + -
343C ILE* 3.7 20.9 - - + -
344C VAL* 3.6 27.1 - - + -
348C TYR* 3.8 16.4 - + + -
564C ILE* 3.7 12.6 - - + -
567C LEU* 4.8 1.3 - - + -
580C PHE* 3.4 23.1 - + + -
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Residues in contact with ALA 202 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198C PHE* 2.9 24.7 + - + +
199C ALA* 3.8 2.9 - - - +
201C PHE* 1.3 76.3 - - - +
203C GLN* 1.3 52.1 + - - +
205C PHE* 4.3 2.0 - - - -
206C THR* 2.5 37.6 + - - +
348C TYR* 3.0 38.7 - - + +
387C TRP* 4.5 2.2 - - + -
390C LEU* 4.9 0.2 - - + -
682C HEM 3.6 22.0 - - + +
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Residues in contact with GLN 203 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199C ALA 3.4 3.1 + - - +
200C PHE* 3.2 33.5 + - - +
201C PHE 2.9 0.6 - - - -
202C ALA* 1.3 78.8 - - - +
204C HIS* 1.3 57.2 + - - +
207C HIS* 2.5 52.6 + - + +
295C VAL* 4.5 0.7 - - - +
298C LEU* 3.1 39.3 - - + +
682C HEM 2.9 69.3 + - + +
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Residues in contact with HIS 204 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200C PHE 3.0 15.9 + - - +
201C PHE* 3.8 7.2 - + - +
203C GLN* 1.3 76.4 - - - +
205C PHE* 1.3 69.2 + - + +
207C HIS 3.3 4.7 + - - -
232C HIS* 3.6 26.9 - + - -
233C ILE* 5.0 1.8 - - + -
292C PHE* 3.0 52.9 - + - -
298C LEU* 3.6 18.1 + - + +
301C TYR* 3.9 20.3 - + + +
302C ALA* 4.0 19.6 + - + -
305C TRP* 3.0 42.2 + + - -
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Residues in contact with PHE 205 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201C PHE* 2.8 30.3 + + + +
202C ALA 4.5 0.2 - - - +
204C HIS* 1.3 80.3 - - + +
206C THR* 1.3 78.1 + - + +
207C HIS 2.9 8.4 + - - -
208C GLN* 3.2 41.4 + - - +
209C PHE* 3.6 22.1 - + - -
228C VAL* 4.3 5.4 - - + -
232C HIS* 4.6 5.2 - - - -
340C THR* 3.8 21.5 - - + -
341C ILE* 6.3 0.2 - - - -
344C VAL* 3.2 51.4 - - + -
348C TYR* 4.5 15.0 - + - -
385C TYR* 5.0 2.9 - - - -
530C SER* 5.3 4.5 - - - -
534C LEU* 4.3 12.8 - - + -
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Residues in contact with THR 206 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202C ALA 2.5 21.9 + - - +
203C GLN* 4.0 0.3 - - - -
205C PHE* 1.3 91.9 - - + +
207C HIS* 1.3 71.8 + - - +
208C GLN 3.1 1.8 + - - -
209C PHE* 3.4 15.8 + - + -
210C PHE* 2.8 53.5 + - + -
348C TYR* 4.2 0.7 - - - +
385C TYR* 3.1 42.1 - - + -
682C HEM 4.4 2.6 - - - +
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Residues in contact with HIS 207 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203C GLN* 2.5 45.2 + - + +
204C HIS 3.5 4.0 - - - +
205C PHE 2.9 2.4 - - - -
206C THR* 1.3 86.4 + - - +
208C GLN* 1.3 60.0 + - - +
210C PHE* 3.2 14.2 - - + +
211C LYS* 3.6 0.7 - - - +
289C GLN* 2.7 31.5 + - - +
291C VAL* 4.6 13.9 - - + -
292C PHE* 3.4 26.5 - + + -
298C LEU* 5.5 1.6 - - + -
682C HEM 3.7 60.6 + + + +
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Residues in contact with GLN 208 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204C HIS 4.0 1.0 + - - -
205C PHE* 3.2 14.2 + - - +
207C HIS* 1.3 78.9 - - - +
209C PHE* 1.3 91.4 + - + +
211C LYS* 3.0 24.1 - - - +
223C GLY* 4.1 3.8 - - - -
227C GLY 4.1 5.4 - - - +
228C VAL* 3.2 37.8 - - - +
229C ASP* 4.2 1.8 - - - +
230C LEU* 3.0 28.0 - - - +
231C ASN* 3.1 23.4 + - - +
232C HIS* 2.8 41.8 + - + +
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Residues in contact with PHE 209 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148C TYR* 4.4 0.3 - - - -
205C PHE* 3.6 36.1 - + - -
206C THR* 3.7 29.2 - - + -
208C GLN* 1.3 107.0 - - + +
210C PHE* 1.3 80.0 + + - +
211C LYS* 3.5 3.1 + - - +
221C THR* 3.9 6.9 + - - -
223C GLY* 4.4 4.2 - - - -
227C GLY* 4.1 20.0 - - - +
228C VAL* 4.0 13.2 - - + -
377C ILE* 2.7 51.5 - - + +
381C PHE* 4.0 18.2 - + - -
385C TYR* 5.7 0.2 - + - -
530C SER* 5.9 2.0 - - - -
534C LEU* 5.6 2.5 - - + -
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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