Contacts of the helix formed by residues 213 - 227 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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211B ASN 3.4 5.9 + - - -
212B PHE* 1.3 80.9 - - - +
214B TYR* 1.3 60.7 + - - +
215B GLU* 3.7 7.3 + - - +
216B THR* 3.1 33.0 + - - -
217B PHE* 3.1 24.1 + - - +
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Residues in contact with TYR 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B ILE 2.5 31.3 + - - -
111B GLU 4.9 1.6 - - - -
113B GLY* 3.2 19.8 - - - -
114B GLU* 3.8 39.0 - - + +
129B LEU* 3.6 22.5 - - + +
160B ALA* 4.7 0.9 - - + -
164B ILE* 4.0 13.5 - - + -
167B LYS* 6.3 0.9 - - - +
212B PHE* 3.8 25.9 + + + -
213B SER* 1.3 70.5 - - - +
215B GLU* 1.3 61.2 + - - +
217B PHE* 3.2 22.3 + + - +
218B GLN* 2.8 53.4 + - + +
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Residues in contact with GLU 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B SER* 2.5 29.8 + - - -
73B TYR* 2.8 29.8 + - - -
213B SER* 3.3 7.3 + - - +
214B TYR* 1.3 80.7 - - - +
216B THR* 1.3 62.9 + - - +
218B GLN* 3.4 8.5 - - - +
219B GLN* 3.2 35.8 + - + +
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Residues in contact with THR 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213B SER* 3.1 26.8 + - - -
214B TYR 3.3 0.6 - - - -
215B GLU* 1.3 79.9 - - - +
217B PHE* 1.3 62.9 + - - +
219B GLN* 3.6 4.1 + - - +
220B LYS* 3.2 43.9 + - + +
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Residues in contact with PHE 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B ILE* 4.0 15.0 - - + -
129B LEU* 4.2 10.5 - - + -
156B LEU* 3.7 40.4 - - + -
157B VAL* 3.8 13.9 - - + -
159B GLU* 5.8 0.7 - - - -
160B ALA* 3.9 15.9 - - + -
212B PHE* 4.1 10.8 - + + -
213B SER 3.1 14.5 + - - +
214B TYR* 3.2 50.2 + + - +
216B THR* 1.3 74.7 - - - +
218B GLN* 1.3 69.2 + - - +
220B LYS* 3.4 8.7 + - - +
221B MET* 3.1 45.9 + - + +
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Residues in contact with GLN 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B PHE* 3.8 17.0 - - + -
73B TYR* 2.9 43.2 + - - +
110B ILE* 3.9 16.6 - - + -
111B GLU* 3.7 27.9 + - - +
114B GLU* 5.6 0.2 + - - -
214B TYR* 2.8 54.0 + - + +
215B GLU* 3.4 13.6 - - - +
216B THR 3.4 0.2 - - - -
217B PHE* 1.3 75.5 - - - +
219B GLN* 1.3 58.4 + - - +
221B MET* 3.1 5.2 + - - +
222B LEU* 3.0 27.7 + - - +
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Residues in contact with GLN 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B PHE* 2.9 29.3 + - - -
69B ARG* 3.6 10.6 + - - +
71B SER* 3.5 9.8 + - - -
73B TYR* 3.3 18.0 + - - -
215B GLU* 3.2 27.4 + - + +
216B THR* 4.1 4.7 - - - +
217B PHE 3.3 0.2 - - - -
218B GLN* 1.3 74.0 - - - +
220B LYS* 1.3 64.0 + - - +
222B LEU* 3.5 15.6 + - - +
223B ARG* 3.0 62.2 + - - +
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Residues in contact with LYS 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156B LEU* 4.3 28.0 - - + -
216B THR* 3.2 37.4 + - + +
217B PHE* 3.7 6.3 - - - +
218B GLN 3.3 0.2 - - - -
219B GLN* 1.3 76.7 - - + +
221B MET* 1.3 59.5 + - - +
223B ARG* 3.4 8.4 + - - +
224B PHE* 3.0 27.2 + - - +
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Residues in contact with MET 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B CYS* 5.2 2.5 - - - -
107B LEU* 5.6 0.7 - - + -
110B ILE* 3.8 25.8 - - + -
136B LEU* 4.7 11.0 - - + -
153B SER* 3.7 39.9 - - - +
156B LEU* 4.4 9.9 - - - -
157B VAL* 3.7 22.7 - - + -
217B PHE* 3.1 39.5 + - + +
218B GLN* 3.1 8.4 + - - +
220B LYS* 1.3 75.0 - - - +
222B LEU* 1.3 65.0 + - - +
224B PHE* 3.3 11.2 + - + +
225B LEU* 3.0 32.6 + - + +
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Residues in contact with LEU 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B LEU* 3.8 31.2 - - + +
68B PHE* 3.6 24.2 - - + -
69B ARG* 3.6 39.3 - - + +
107B LEU* 3.9 22.4 - - + +
218B GLN 3.0 15.8 + - - +
219B GLN* 3.7 13.7 - - - +
220B LYS 3.3 0.2 - - - -
221B MET* 1.3 75.6 - - - +
223B ARG* 1.3 59.5 + - - +
225B LEU* 3.2 5.1 + - + +
226B GLU* 2.9 50.7 + - + +
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Residues in contact with ARG 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B ARG* 4.2 24.7 + - - +
219B GLN* 3.0 44.6 + - - +
220B LYS* 3.8 7.4 - - - +
222B LEU* 1.3 75.2 - - + +
224B PHE* 1.3 65.5 + - - +
226B GLU* 4.0 22.4 + - - +
227B SER* 3.3 21.7 + - - -
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Residues in contact with PHE 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136B LEU* 4.0 12.8 - - + -
139B ILE* 5.4 3.8 - - + -
145B LEU* 4.8 1.8 - - + -
149B VAL* 3.7 20.6 - - + -
150B VAL* 4.3 20.2 - - + -
153B SER* 3.4 36.8 - - - -
220B LYS 3.0 14.5 + - - +
221B MET* 3.4 14.4 - - + +
223B ARG* 1.3 77.6 - - - +
225B LEU* 1.3 84.1 + - + +
227B SER* 2.6 27.8 + - - -
228B HIS* 3.3 32.4 - + - -
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Residues in contact with LEU 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B VAL* 4.3 22.3 - - + +
106B CYS* 4.2 18.8 - - + -
107B LEU* 3.8 33.9 - - + -
110B ILE* 4.8 3.6 - - + -
136B LEU* 4.5 6.5 - - + -
139B ILE* 4.0 29.8 - - + -
143B PHE* 5.7 0.3 - - - -
221B MET* 3.0 23.1 + - + +
222B LEU* 3.7 5.2 - - + +
224B PHE* 1.3 97.2 - - + +
226B GLU* 1.3 62.8 + - + +
227B SER 3.3 0.9 + - - -
228B HIS* 3.3 15.6 + - + +
229B LEU* 3.5 16.3 - - + +
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Residues in contact with GLU 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B LEU* 4.5 14.8 - - + +
69B ARG* 2.2 45.3 + - - -
222B LEU* 2.9 41.5 + - + +
223B ARG* 4.0 17.5 + - - +
224B PHE 3.3 0.2 - - - -
225B LEU* 1.3 76.0 - - + +
227B SER* 1.3 60.2 + - - +
228B HIS 3.1 1.9 + - - -
229B LEU* 3.2 28.5 + - + +
301B GOL 4.0 10.8 + - - +
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Residues in contact with SER 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223B ARG 3.3 12.4 + - - -
224B PHE* 2.6 25.2 + - - -
225B LEU 3.1 0.2 - - - -
226B GLU* 1.3 75.7 - - - +
228B HIS* 1.3 76.3 + - - +
229B LEU 3.4 1.1 - - - -
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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