Contacts of the helix formed by residues 207 - 219 (chain c) in PDB entry 3J7Y
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 GLY 207 (chain c).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203c LEU* 3.7 15.4 + - - -
206c SER* 1.3 86.9 + - - +
208c PRO* 1.4 66.8 - - - +
209c GLU 3.4 2.5 - - - -
210c ARG* 3.7 4.7 + - - +
211c THR* 2.7 30.4 + - - -
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Residues in contact with PRO 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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132c PHE* 3.5 18.3 - - + -
203c LEU* 3.8 19.5 - - + +
207c GLY* 1.4 81.5 - - - +
209c GLU* 1.3 67.3 + - + +
211c THR* 2.6 18.8 + - - +
212c ALA* 2.9 17.9 + - - +
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Residues in contact with GLU 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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207c GLY 3.4 0.4 - - - -
208c PRO* 1.3 84.2 - - + +
210c ARG* 1.3 59.0 + - - +
212c ALA* 3.2 8.6 + - - +
213c LEU* 2.9 36.4 + - + +
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Residues in contact with ARG 210 (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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21b ARG* 4.5 10.6 + - - +
80c GLN 2.7 28.3 + - - -
81c GLU* 3.4 30.6 - - + +
82c ASN* 4.6 9.3 + - - -
202c LEU* 4.7 1.1 - - + -
206c SER* 3.4 33.8 - - - +
207c GLY* 3.7 5.6 + - - +
208c PRO 3.2 0.2 - - - -
209c GLU* 1.3 80.1 - - - +
211c THR* 1.3 56.5 - - - +
213c LEU* 3.2 20.2 + - - +
214c PHE* 2.9 28.5 + - - +
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Residues in contact with THR 211 (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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132c PHE* 3.5 16.0 - - - -
199c ILE* 3.4 19.3 - - + +
202c LEU* 3.7 17.0 - - + -
203c LEU* 3.2 36.8 - - + +
207c GLY 2.7 14.3 + - - +
208c PRO* 2.6 23.4 + - - +
210c ARG* 1.3 78.8 - - - +
212c ALA* 1.3 54.7 + - - +
214c PHE* 3.2 8.0 + - - +
215c ILE* 2.9 34.9 + - - +
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Residues in contact with ALA 212 (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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132c PHE* 4.2 0.6 - - + -
136c CYS* 3.8 27.8 - - - -
140c PHE* 4.2 20.4 - - + -
208c PRO 2.9 12.9 + - - +
209c GLU* 3.2 12.8 + - - +
211c THR* 1.3 75.1 - - - +
213c LEU* 1.3 57.8 - - + +
215c ILE* 3.2 5.5 + - - +
216c ARG* 2.9 28.6 + - - +
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Residues in contact with LEU 213 (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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21b ARG* 5.0 7.2 - - - +
140c PHE* 5.9 3.4 - - + -
209c GLU* 2.9 19.0 + - + +
210c ARG* 3.4 23.3 - - - +
212c ALA* 1.3 76.3 - - + +
214c PHE* 1.3 56.3 + - - +
216c ARG* 3.2 44.5 + - - +
217c ASP* 2.9 35.1 + - - +
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Residues in contact with PHE 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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21b ARG* 3.6 22.4 - - - +
79c LEU* 3.5 31.6 - - + -
81c GLU* 3.5 16.2 - - - -
173c LEU* 4.3 11.9 - - + -
195c PHE* 4.2 22.4 - + - -
198c VAL* 5.8 6.7 - - + -
199c ILE* 4.5 11.2 - - + -
202c LEU* 4.0 18.4 - - + -
210c ARG 2.9 12.6 + - - +
211c THR* 3.3 9.9 - - + +
213c LEU* 1.3 76.9 - - - +
215c ILE* 1.3 66.7 + - + +
217c ASP* 3.2 7.2 + - - +
218c PHE* 2.9 55.2 + + + +
219c LEU* 6.2 0.9 - - + -
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Residues in contact with ILE 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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132c PHE* 3.6 28.0 - - + -
133c SER* 3.9 20.2 - - - +
136c CYS* 4.2 12.3 - - + -
137c LEU* 3.9 24.9 - - + -
140c PHE* 6.0 0.9 - - + -
199c ILE* 4.3 17.3 - - + -
211c THR 2.9 19.5 + - - +
212c ALA* 3.4 7.2 - - - +
214c PHE* 1.3 82.6 - - + +
216c ARG* 1.3 60.2 + - - +
219c LEU* 2.9 56.6 + - + +
220c ILE* 3.3 7.8 + - + -
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Residues in contact with ARG 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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20b GLY 5.2 2.6 + - - -
140c PHE* 4.5 21.1 - - + -
212c ALA 2.9 13.2 + - - +
213c LEU* 3.3 36.2 + - - +
215c ILE* 1.3 78.0 - - - +
217c ASP* 1.3 88.5 + - - +
218c PHE 3.4 0.2 + - - -
220c ILE* 3.6 31.6 - - + +
221c THR* 3.7 10.9 + - - +
314c TRP* 4.1 23.6 - - + +
315c ASN 4.1 5.9 + - - -
316c TYR* 3.6 53.7 + - + +
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Residues in contact with ASP 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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15b LEU 5.7 0.3 - - - +
16b HIS 5.2 2.8 - - - +
20b GLY* 3.0 27.2 + - - +
21b ARG* 2.8 43.0 + - + +
213c LEU* 2.9 17.1 + - - +
214c PHE 3.2 9.8 + - - +
216c ARG* 1.3 101.4 + - - +
218c PHE* 1.3 66.2 + - + +
221c THR* 2.6 32.5 + - - +
316c TYR* 4.0 1.1 - - - -
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Residues in contact with PHE 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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15b LEU* 4.2 16.7 - - + +
21b ARG* 3.9 24.9 - - + -
23b VAL* 4.1 21.3 - - + -
79c LEU* 4.3 8.3 - - + -
169c VAL* 4.0 21.9 - - + +
173c LEU* 3.4 47.8 - - + -
195c PHE* 5.1 0.7 - - + -
214c PHE* 2.9 48.9 + + + +
215c ILE 3.2 0.4 + - - -
217c ASP* 1.3 85.3 - - + +
219c LEU* 1.3 68.3 + - + +
220c ILE 3.5 0.2 - - - -
221c THR* 2.9 15.2 + - - -
222c GLN* 3.8 13.3 + - - +
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Residues in contact with LEU 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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133c SER* 4.7 10.3 - - - -
137c LEU* 4.7 11.9 - - + -
160c LEU* 3.5 22.3 - - + +
161c THR* 4.9 2.5 - - + -
165c VAL* 4.9 1.7 - - + +
166c VAL* 4.1 30.5 - - + -
169c VAL* 5.1 6.1 - - + -
195c PHE* 4.7 22.0 - - + -
196c PHE* 4.8 5.6 - - + -
199c ILE* 4.4 13.5 - - + -
214c PHE* 6.2 0.7 - - + -
215c ILE* 2.9 46.3 + - + +
218c PHE* 1.3 77.0 - - + +
220c ILE* 1.3 63.0 + - + +
222c GLN* 3.2 25.0 + - - +
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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