Contacts of the helix formed by residues 207 - 219 (chain X) 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 THR 207 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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695 TRP* 5.6 6.5 - - + +
28X TYR* 2.8 15.4 + - - -
32X LEU* 5.4 0.7 - - - -
156X LYS* 4.7 22.0 - - + +
206X LEU* 1.3 75.7 - - - +
208X LEU* 1.3 64.3 + - - +
209X GLU* 3.6 4.9 + - - +
210X GLU* 3.1 42.7 + - + +
211X ALA* 3.4 11.8 + - - +
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Residues in contact with LEU 208 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16X LEU* 4.1 18.8 - - + -
21X CYS* 4.3 10.1 - - - -
24X LEU* 4.3 12.6 - - + -
28X TYR* 3.6 5.8 - - - +
32X LEU* 4.2 29.0 - - + +
207X THR* 1.3 74.2 - - - +
209X GLU* 1.3 60.8 - - - +
211X ALA* 3.2 3.3 + - - +
212X ILE* 2.9 48.9 + - + +
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Residues in contact with GLU 209 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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635 LYS* 3.0 24.8 + - - -
695 TRP* 2.7 58.4 + - + +
705 LEU* 4.7 2.3 - - - +
207X THR* 3.6 4.4 + - - +
208X LEU* 1.3 80.1 - - - +
210X GLU* 1.3 56.0 - - - +
212X ILE* 3.2 27.4 + - + +
213X GLU* 2.9 29.2 + - - +
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Residues in contact with GLU 210 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495 VAL* 5.6 3.8 - - - +
585 ILE* 3.6 31.5 + - + +
695 TRP* 6.1 0.2 - - + -
705 LEU* 3.8 31.4 - - + +
715 ALA* 4.6 6.1 + - - +
156X LYS* 4.3 23.5 + - - +
163X ARG* 4.5 7.4 + - - -
205X GLY 4.9 0.7 - - - +
206X LEU* 3.4 30.0 - - + +
207X THR* 3.1 35.2 + - + +
209X GLU* 1.3 77.4 - - + +
211X ALA* 1.3 58.7 + - - +
213X GLU* 3.2 5.0 + - - +
214X LYS* 2.9 28.4 + - - +
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Residues in contact with ALA 211 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24X LEU* 3.5 7.3 - - + +
28X TYR* 3.2 35.9 - - + +
203X TRP* 3.4 22.2 - - + -
206X LEU* 4.1 8.7 - - + +
207X THR 3.4 9.9 + - - +
208X LEU 3.2 9.5 + - - +
210X GLU* 1.3 81.1 - - - +
212X ILE* 1.3 57.0 + - - +
214X LYS* 3.2 5.0 + - - +
215X GLN 2.9 24.4 + - - -
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Residues in contact with ILE 212 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20X ILE* 3.9 25.8 - - + +
21X CYS* 3.5 31.0 - - - -
24X LEU* 4.3 8.5 - - + -
208X LEU* 2.9 34.7 + - + +
209X GLU* 3.4 26.9 - - + +
211X ALA* 1.3 76.0 - - - +
213X GLU* 1.3 58.7 + - - +
215X GLN* 3.2 9.5 + - - +
216X ARG* 2.9 29.7 + - + +
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Residues in contact with GLU 213 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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585 ILE* 3.9 11.2 - - + +
595 THR 4.4 4.7 - - - +
625 GLY* 4.3 4.0 - - - -
635 LYS* 3.6 26.0 - - - +
705 LEU* 3.7 29.8 - - + -
209X GLU 2.9 12.1 + - - +
210X GLU 3.2 8.9 + - - +
212X ILE* 1.3 78.3 - - - +
214X LYS* 1.3 56.9 - - - +
216X ARG* 3.2 37.0 + - - +
217X LEU* 2.9 51.3 + - - +
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Residues in contact with LYS 214 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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565 GLU* 5.9 1.5 + - - -
585 ILE* 3.8 25.7 - - + +
163X ARG* 5.8 1.3 - - - +
202X GLU* 3.1 48.8 + - - +
203X TRP* 3.7 29.5 - - + +
206X LEU* 4.3 2.2 - - + -
210X GLU 2.9 13.8 + - - +
211X ALA* 3.2 9.4 + - - +
213X GLU* 1.3 77.1 - - - +
215X GLN* 1.3 56.8 + - - +
217X LEU* 3.2 14.3 + - + +
218X LEU* 2.9 56.4 + - + +
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Residues in contact with GLN 215 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20X ILE* 3.2 27.6 - - + +
23X ARG* 3.3 35.6 + - - +
24X LEU* 3.6 26.7 - - + +
25X PRO* 5.9 0.2 - - - +
203X TRP* 4.1 11.5 - - + -
211X ALA 2.9 13.0 + - - +
212X ILE* 3.2 10.5 + - - +
214X LYS* 1.3 77.0 - - - +
216X ARG* 1.3 62.9 + - - +
218X LEU* 3.2 15.8 + - - +
219X GLU* 3.0 35.1 + - - +
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Residues in contact with ARG 216 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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625 GLY* 3.0 32.7 + - - -
635 LYS* 3.4 28.2 - - - +
20X ILE* 4.9 10.0 - - + +
212X ILE* 2.9 15.6 + - + +
213X GLU* 3.4 23.7 + - - +
215X GLN* 1.3 78.7 + - - +
217X LEU* 1.3 59.1 + - - +
219X GLU* 3.2 12.9 + - - +
220X GLU* 2.9 60.2 + - + +
167Y ALA* 5.8 4.8 + - - +
169Y ARG* 6.1 0.6 - - - +
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Residues in contact with LEU 217 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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585 ILE* 5.1 12.6 - - + -
595 THR 5.4 2.7 - - - +
625 GLY* 3.9 21.8 - - - -
213X GLU* 2.9 36.9 + - - +
214X LYS* 3.2 16.4 + - + +
216X ARG* 1.3 82.7 - - - +
218X LEU* 1.3 67.2 + - + +
220X GLU* 3.6 27.4 + - - +
221X LYS 5.0 1.0 + - - -
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Residues in contact with LEU 218 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202X GLU* 5.8 0.4 - - - +
203X TRP* 4.3 24.2 - - + -
214X LYS* 2.9 40.3 + - + +
215X GLN* 3.2 16.6 + - - +
217X LEU* 1.3 80.7 - - + +
219X GLU* 1.3 58.8 + - + +
220X GLU 3.7 1.4 + - - -
221X LYS* 4.6 12.1 - - - +
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Residues in contact with GLU 219 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20X ILE* 4.3 10.8 - - - +
23X ARG* 4.3 23.9 + - - -
215X GLN* 3.0 40.1 + - - +
216X ARG* 3.4 10.8 - - - +
218X LEU* 1.3 76.2 - - + +
220X GLU* 1.3 63.8 + - - +
221X LYS* 3.9 12.0 - - - +
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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