Contacts of the helix formed by residues 208 - 223 (chain C) in PDB entry 1RJF
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 HIS 208 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177C ASN* 5.4 0.8 + - - +
206C TYR 4.8 3.4 - - - -
207C MET* 1.3 82.4 - - - +
209C ASN* 1.3 62.7 + - - +
210C ASN 3.7 0.9 - - - +
211C GLU* 3.9 32.3 + - - +
212C SER* 2.8 25.5 + - - -
258C GLU* 3.8 24.2 + - + -
260C PRO* 3.9 22.0 - - + +
261C THR* 3.5 7.6 - - - -
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Residues in contact with ASN 209 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208C HIS* 1.3 76.4 - - - +
210C ASN* 1.3 58.7 + - + +
212C SER* 2.7 20.5 + - - -
213C GLN* 3.1 14.6 + - - +
261C THR* 3.3 15.9 - - + +
264C THR* 4.6 12.5 - - + +
265C TYR* 2.7 41.5 + - - -
274C ARG* 4.7 0.6 - - - +
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Residues in contact with ASN 210 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208C HIS* 4.9 0.2 - - - +
209C ASN* 1.3 77.6 - - + +
211C GLU* 1.3 65.6 + - - +
212C SER 3.3 0.7 - - - -
213C GLN* 3.8 12.2 - - - +
214C LEU* 3.2 30.8 + - - +
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Residues in contact with GLU 211 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176C LEU 5.4 1.4 - - - +
177C ASN* 4.2 39.5 + - + +
179C ILE* 5.7 0.5 - - - +
207C MET* 3.6 10.7 - - + +
208C HIS* 3.8 34.7 + - - +
209C ASN 3.3 0.2 - - - -
210C ASN* 1.3 82.4 + - - +
212C SER* 1.3 59.3 + - - +
214C LEU* 3.7 11.1 + - + +
215C LEU* 3.4 16.1 + - - +
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Residues in contact with SER 212 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204C LEU* 4.1 13.7 - - - -
207C MET* 3.6 21.3 - - - +
208C HIS 2.8 14.4 + - - -
209C ASN* 2.7 21.8 + - - -
211C GLU* 1.3 77.6 - - - +
213C GLN* 1.3 58.9 + - - +
214C LEU 3.2 1.8 - - - -
215C LEU* 3.3 3.5 + - - +
216C ILE* 3.1 37.7 + - - +
274C ARG* 3.2 27.9 + - - -
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Residues in contact with GLN 213 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209C ASN* 3.1 18.1 + - - +
210C ASN* 4.1 14.8 - - - +
211C GLU 3.5 0.2 - - - -
212C SER* 1.3 76.6 + - - +
214C LEU* 1.3 59.0 + - - +
216C ILE* 4.0 6.9 - - - +
217C ASN* 2.8 60.8 + - - +
265C TYR* 4.1 6.8 + - - -
274C ARG* 3.0 55.4 + - - +
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Residues in contact with LEU 214 (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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177C ASN 5.4 5.8 - - - +
179C ILE* 3.8 35.1 - - + +
210C ASN* 3.2 25.9 + - - +
211C GLU* 3.8 11.0 - - + +
212C SER 3.2 0.2 - - - -
213C GLN* 1.3 78.8 - - - +
215C LEU* 1.3 56.7 + - - +
217C ASN* 5.0 2.7 - - + +
218C THR* 2.6 42.1 + - - +
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Residues in contact with LEU 215 (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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104C LEU* 4.9 6.1 - - + -
176C LEU* 4.1 23.8 - - + +
179C ILE* 3.8 22.6 - - + +
182C THR* 4.0 15.0 - - + -
203C LEU* 4.7 9.0 - - + -
204C LEU* 4.1 14.4 - - + -
207C MET* 3.8 25.6 - - + -
211C GLU 3.4 11.4 + - - +
212C SER* 3.3 9.5 + - - +
214C LEU* 1.3 80.2 - - - +
216C ILE* 1.3 60.5 + - - +
218C THR 4.2 0.2 - - - -
219C ILE* 3.3 47.1 + - + +
228C TRP* 3.6 4.3 - - + -
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Residues in contact with ILE 216 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204C LEU* 4.3 11.2 - - + -
212C SER* 3.1 23.6 + - - +
213C GLN* 4.3 7.4 - - - +
214C LEU 3.3 0.2 - - - -
215C LEU* 1.3 78.3 - - - +
217C ASN* 1.3 66.6 + - - +
220C MET* 3.3 35.7 + - + +
228C TRP* 3.8 14.8 - - + -
274C ARG* 4.2 29.2 - - + +
275C TRP* 3.2 64.6 - - + +
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Residues in contact with ASN 217 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213C GLN* 2.8 48.0 + - - +
214C LEU* 4.6 3.3 - - + +
216C ILE* 1.3 78.2 - - - +
218C THR* 1.3 59.6 + - - +
220C MET* 4.2 9.4 - - - +
221C SER* 2.7 32.8 + - - +
274C ARG 4.6 2.4 - - - +
277C ALA* 4.9 9.0 - - - +
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Residues in contact with THR 218 (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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179C ILE* 3.8 18.9 - - + +
183C THR* 3.4 33.9 - - + -
214C LEU* 2.6 31.8 + - - +
215C LEU 4.5 0.7 - - - -
216C ILE 3.3 0.6 - - - -
217C ASN* 1.3 78.2 - - - +
219C ILE* 1.3 62.0 + - + +
221C SER* 3.4 4.7 + - - -
222C LYS* 3.1 36.2 + - + +
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Residues in contact with ILE 219 (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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102C VAL* 6.1 1.3 - - + -
104C LEU* 3.8 29.4 - - + -
179C ILE* 5.9 0.4 - - + -
182C THR* 4.9 2.9 - - + -
183C THR* 6.2 0.7 - - + -
186C LEU* 4.1 21.8 - - + -
198C VAL* 3.7 22.9 - - + -
215C LEU* 3.3 43.9 + - + +
218C THR* 1.3 77.0 - - + +
220C MET* 1.3 64.8 + - - +
222C LYS* 3.3 10.4 + - - +
223C PHE* 3.3 32.3 - - + -
228C TRP* 3.7 17.9 - - + -
328C TRP* 4.6 1.0 - - + -
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Residues in contact with MET 220 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216C ILE* 3.3 28.4 + - + +
217C ASN* 4.4 7.6 - - - +
219C ILE* 1.3 78.1 - - - +
221C SER* 1.3 58.4 + - - +
223C PHE 3.0 21.8 - - - +
228C TRP* 3.9 9.0 - - + -
274C ARG 4.9 0.4 - - - +
275C TRP* 3.7 35.7 - - + -
277C ALA* 4.1 25.4 - - + -
278C ALA* 4.2 12.6 - - - +
328C TRP* 3.2 59.4 + - + +
330C HIS* 4.0 3.1 + - - -
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Residues in contact with SER 221 (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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192C ARG* 3.1 21.4 + - - -
217C ASN 2.7 23.3 + - - -
218C THR* 3.8 5.6 - - - -
219C ILE 3.3 0.8 - - - -
220C MET* 1.3 77.5 - - - +
222C LYS* 1.3 60.1 + - - +
223C PHE 3.3 0.6 + - - -
330C HIS* 3.3 23.4 - - - -
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Residues in contact with LYS 222 (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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183C THR* 3.4 34.0 + - + -
186C LEU* 3.9 17.6 + - + +
187C ASP* 2.8 44.6 + - - +
190C THR* 5.4 0.2 + - - -
192C ARG* 3.4 45.3 + - - +
218C THR* 3.1 23.6 + - + +
219C ILE* 3.3 8.7 + - - +
220C MET 3.3 0.6 - - - -
221C SER* 1.3 78.8 - - - +
223C PHE* 1.3 75.7 + - + +
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Residues in contact with PHE 223 (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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100C GLN* 3.4 9.9 - - - -
102C VAL* 5.0 3.6 - - + -
186C LEU* 4.7 15.0 - - + -
190C THR* 3.5 27.4 - - + -
191C LYS 3.3 27.4 - - - -
192C ARG* 3.7 8.5 - - - +
196C THR* 3.4 33.7 - - + +
198C VAL* 5.0 2.0 - - + -
219C ILE* 3.3 39.1 + - + +
220C MET 3.0 17.6 - - - +
221C SER 4.7 0.9 - - - -
222C LYS* 1.3 95.5 - - + +
224C SER* 1.3 64.2 + - - +
225C HIS 4.1 13.9 - - - +
328C TRP* 3.4 11.9 + + + -
330C HIS* 3.8 9.6 + - - -
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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