Contacts of the helix formed by residues 213 - 227 (chain C) in PDB entry 4RQI
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 SER 213 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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211C ASN 3.4 5.6 + - - -
212C PHE* 1.3 79.7 - - - +
214C TYR* 1.3 63.7 + - - +
215C GLU* 3.6 8.7 + - - +
216C THR* 3.2 32.9 + - - -
217C PHE* 3.1 20.8 + - - +
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Residues in contact with TYR 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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110C ILE 2.5 31.4 + - - -
111C GLU 5.0 1.6 - - - -
113C GLY* 3.1 18.6 - - - -
114C GLU* 3.6 47.1 - - + +
129C LEU* 3.6 23.7 - - + +
160C ALA* 4.6 0.7 - - + -
164C ILE* 4.0 7.6 - - + -
167C LYS* 6.1 0.6 - - - +
212C PHE* 3.7 26.2 + + + -
213C SER* 1.3 70.7 + - - +
215C GLU* 1.3 59.6 - - - +
217C PHE* 3.2 23.0 + + - +
218C GLN* 2.8 59.3 + - + +
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Residues in contact with GLU 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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71C SER* 2.7 25.8 + - - -
73C TYR* 2.5 31.5 + - - -
213C SER* 3.2 8.0 + - - +
214C TYR* 1.3 79.6 - - - +
216C THR* 1.3 63.1 + - - +
218C GLN* 3.3 9.1 + - - +
219C GLN* 3.2 39.0 + - + +
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Residues in contact with THR 216 (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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213C SER* 3.2 26.8 + - - -
214C TYR 3.3 0.6 - - - -
215C GLU* 1.3 79.1 - - - +
217C PHE* 1.3 62.4 + - - +
219C GLN* 3.6 4.7 + - - +
220C LYS* 3.2 41.7 + - + +
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Residues in contact with PHE 217 (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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110C ILE* 4.1 12.3 - - + -
129C LEU* 4.0 12.3 - - + -
156C LEU* 3.4 44.2 - - + -
157C VAL* 3.6 14.6 - - + -
159C GLU* 6.0 0.4 - - - -
160C ALA* 3.6 20.4 - - + -
212C PHE* 4.1 11.9 - + + -
213C SER 3.1 13.5 + - - +
214C TYR* 3.2 45.3 + + - +
216C THR* 1.3 75.6 - - - +
218C GLN* 1.3 66.5 + - - +
220C LYS* 3.4 8.6 + - - +
221C MET* 3.2 42.9 + - + +
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Residues in contact with GLN 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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68C PHE* 3.7 21.3 - - + -
73C TYR* 2.9 41.0 + - - +
110C ILE* 3.8 15.5 - - + -
111C GLU* 3.8 26.3 + - - +
114C GLU* 5.4 0.8 + - - -
214C TYR* 2.8 51.1 + - + +
215C GLU* 3.3 15.0 - - - +
216C THR 3.4 0.2 - - - -
217C PHE* 1.3 77.3 - - + +
219C GLN* 1.3 58.4 + - - +
221C MET* 3.1 5.8 + - - +
222C LEU 2.9 23.9 + - - -
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Residues in contact with GLN 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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68C PHE* 3.0 29.3 + - - -
69C ARG* 3.6 21.3 + - - +
71C SER* 3.5 5.2 + - - -
73C TYR* 3.0 21.0 + - - -
215C GLU* 3.2 33.3 + - + +
216C THR* 4.2 4.7 - - - +
218C GLN* 1.3 76.7 - - - +
220C LYS* 1.3 65.0 + - - +
222C LEU* 3.5 5.5 + - - +
223C ARG* 2.7 61.1 + - - +
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Residues in contact with LYS 220 (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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156C LEU* 3.8 35.4 - - + +
216C THR* 3.2 36.5 + - + +
217C PHE* 3.6 7.2 - - - +
218C GLN 3.2 0.2 - - - -
219C GLN* 1.3 76.4 - - - +
221C MET* 1.3 58.0 + - - +
223C ARG* 3.4 6.6 + - - +
224C PHE* 2.9 30.2 + - - +
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Residues in contact with MET 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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106C CYS* 5.0 0.9 - - - -
107C LEU* 5.5 0.7 - - + -
110C ILE* 3.8 24.5 - - + -
136C LEU* 4.6 12.3 - - + -
153C SER* 3.7 40.2 - - - +
156C LEU* 4.3 10.1 - - - -
157C VAL* 3.6 22.0 - - + -
217C PHE* 3.2 36.3 + - + +
218C GLN* 3.1 9.7 + - - +
220C LYS* 1.3 75.8 - - - +
222C LEU* 1.3 58.8 + - - +
224C PHE* 3.3 11.2 + - + +
225C LEU* 2.9 40.6 + - + +
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Residues in contact with LEU 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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65C LEU* 3.6 32.5 - - + +
68C PHE* 3.7 20.4 - - + -
69C ARG* 3.7 43.3 - - + +
107C LEU* 3.9 21.4 - - + +
218C GLN 2.9 12.2 + - - +
219C GLN* 3.7 15.0 - - - +
221C MET* 1.3 76.5 - - - +
223C ARG* 1.3 59.9 + - - +
225C LEU* 3.4 3.2 + - + +
226C GLU* 2.9 53.3 + - + +
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Residues in contact with ARG 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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69C ARG* 3.7 38.0 + - - +
219C GLN* 2.7 70.2 + - - +
220C LYS* 3.8 4.9 - - - +
222C LEU* 1.3 76.7 - - + +
224C PHE* 1.3 67.3 + - - +
226C GLU* 4.1 10.0 - - - +
227C SER* 3.4 19.2 + - - -
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Residues in contact with PHE 224 (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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136C LEU* 4.3 17.0 - - + -
139C ILE* 5.9 1.8 - - + -
145C LEU* 5.1 2.2 - - + -
149C VAL* 3.6 25.8 - - + -
150C VAL* 4.2 15.3 - - + -
152C SER* 5.2 3.1 - - - -
153C SER* 3.1 39.5 - - - -
156C LEU* 6.6 0.2 - - + -
220C LYS 2.9 18.2 + - - +
221C MET* 3.3 11.0 + - + +
223C ARG* 1.3 77.2 - - - +
225C LEU* 1.3 75.0 + - + +
227C SER* 2.5 28.8 + - - -
228C HIS* 3.4 32.3 - + - -
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Residues in contact with LEU 225 (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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103C VAL* 4.3 22.3 - - + +
106C CYS* 4.1 20.4 - - + -
107C LEU* 3.9 31.9 - - + -
110C ILE* 4.9 3.1 - - + -
136C LEU* 4.3 12.1 - - + -
139C ILE* 4.0 29.6 - - + -
221C MET* 2.9 24.4 + - + +
222C LEU* 3.8 4.3 - - + +
224C PHE* 1.3 91.2 - - + +
226C GLU* 1.3 64.0 + - + +
227C SER 3.2 0.7 + - - -
228C HIS* 3.2 18.3 + - + +
229C LEU* 3.8 13.6 - - - +
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Residues in contact with GLU 226 (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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65C LEU* 4.1 25.9 - - + +
69C ARG* 2.2 38.4 + - - +
103C VAL* 6.4 0.4 - - + -
222C LEU* 2.9 44.6 + - + +
223C ARG* 4.1 7.4 - - - +
224C PHE 3.4 0.4 - - - -
225C LEU* 1.3 76.1 - - + +
227C SER* 1.3 61.2 + - - +
228C HIS 3.1 2.5 + - - -
229C LEU* 3.3 27.0 + - + +
231C ASP* 5.3 1.3 - - - +
301C GOL 3.5 20.4 + - - -
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Residues in contact with SER 227 (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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223C ARG 3.4 10.7 + - - -
224C PHE* 2.5 25.2 + - - -
225C LEU 3.1 0.2 - - - -
226C GLU* 1.3 77.3 - - - +
228C HIS* 1.3 75.3 + - - +
229C LEU 3.5 0.9 - - - -
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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