Contacts of the helix formed by residues 206 - 221 (chain B) in PDB entry 1K7E
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 ARG 206 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B ARG* 2.9 21.9 + - - +
203B GLU* 2.9 55.8 + - - +
205B GLN* 1.3 79.0 - - - +
207B MET* 1.4 65.8 + - + +
208B ILE 2.8 7.7 + - - -
209B GLY* 3.2 3.3 + - - -
210B GLU* 2.8 49.8 + - - +
239B GLY* 3.6 9.5 - - - +
242B ALA* 3.8 23.7 + - + +
243B ASP* 3.6 41.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 207 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B PHE* 4.0 12.1 - - + -
49B LEU* 3.6 26.2 - - + -
55B ARG* 3.4 26.9 - - - +
89B ASN* 3.8 15.3 - - - +
203B GLU 4.6 3.4 - - - +
204B PHE* 3.3 33.0 - - - +
205B GLN* 3.7 9.0 - - - +
206B ARG* 1.4 81.6 - - + +
208B ILE* 1.3 62.9 + - - +
209B GLY 3.3 0.2 - - - -
210B GLU* 3.7 16.6 - - - +
211B GLU* 2.9 37.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 208 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B ARG* 4.1 9.0 - - - +
76B LYS* 3.5 15.0 - - + +
78B GLU* 3.8 29.4 - - + +
86B HIS* 4.1 9.6 - - + -
89B ASN* 4.0 8.7 - - - +
205B GLN* 3.3 33.7 - - - +
206B ARG 2.8 0.8 - - - -
207B MET* 1.3 80.0 - - + +
209B GLY* 1.4 56.6 + - - +
212B THR* 2.8 36.1 + - - -
236B ASN* 4.5 8.5 - - - +
239B GLY* 3.8 4.0 - - - +
240B MET* 3.9 15.7 - - - -
375B ASN* 3.8 29.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 209 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B ARG 3.2 1.1 + - - -
208B ILE* 1.4 79.5 - - - +
210B GLU* 1.3 64.6 + - - +
212B THR* 3.1 2.1 + - - -
213B LYS* 3.0 23.0 + - - +
239B GLY 3.1 9.9 + - - -
240B MET* 3.5 32.1 - - - -
243B ASP* 4.1 10.3 - - - -
244B PHE* 4.0 4.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 210 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B ARG* 2.8 48.9 + - - +
207B MET* 4.0 13.8 - - - +
209B GLY* 1.3 74.5 - - - +
211B GLU* 1.3 63.9 + - + +
213B LYS* 3.4 2.6 + - - +
214B ALA* 3.3 20.6 + - - +
243B ASP* 3.7 30.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 211 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B ARG* 2.7 50.5 + - - +
56B PRO* 3.1 21.8 - - + +
57B THR 3.0 11.6 + - - -
76B LYS* 2.9 19.9 + - - +
207B MET* 2.9 22.0 + - + +
208B ILE 3.9 0.2 - - - +
210B GLU* 1.3 75.6 - - + +
212B THR* 1.4 69.4 + - - +
213B LYS 3.2 0.2 + - - -
214B ALA* 3.2 5.4 + - - -
215B GLN* 2.8 35.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 212 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B LEU* 4.2 8.2 - - + +
76B LYS* 3.7 15.6 - - - +
208B ILE 2.8 25.1 + - - -
209B GLY 3.5 5.2 - - - -
211B GLU* 1.4 76.4 - - - +
213B LYS* 1.3 53.2 + - - +
215B GLN* 3.0 9.4 + - - +
216B ILE* 2.7 40.6 + - + +
240B MET* 3.6 25.1 - - + -
244B PHE* 4.2 8.3 - - + -
373B VAL* 3.8 37.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 213 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B GLY 3.0 15.0 + - - +
210B GLU 3.8 4.7 - - - +
212B THR* 1.3 77.4 - - - +
214B ALA* 1.3 66.6 + - - +
216B ILE* 3.5 3.6 - - - +
217B LEU* 2.9 36.0 + - + +
223B LEU* 3.8 21.1 - - + -
243B ASP* 3.0 34.7 + - - +
244B PHE* 3.7 24.9 - - + -
247B ASP* 3.0 32.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 214 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B GLU 3.3 9.8 + - - +
211B GLU* 3.2 10.1 + - - +
213B LYS* 1.3 83.8 - - - +
215B GLN* 1.3 63.2 + - + +
217B LEU* 3.9 7.9 - - - +
218B ASP* 3.0 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 215 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B PRO* 4.8 8.9 - - - +
57B THR 3.0 22.0 + - - -
58B ALA* 3.9 2.4 - - - +
59B LEU* 3.6 35.3 - - + +
76B LYS* 2.8 25.8 + - - +
211B GLU* 2.8 32.9 + - - +
212B THR* 3.6 6.2 + - - +
214B ALA* 1.3 81.1 - - + +
216B ILE* 1.3 62.7 + - - +
218B ASP* 3.3 4.9 + - - +
219B LYS* 2.9 39.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 216 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B LEU* 3.8 12.6 - - + -
74B TYR* 3.6 37.7 - - + -
212B THR* 2.7 15.9 + - + +
213B LYS* 3.5 11.7 - - - +
215B GLN* 1.3 76.8 - - - +
217B LEU* 1.3 69.5 + - + +
219B LYS* 4.9 0.2 - - - -
220B GLU* 2.9 34.8 + - + +
221B GLY 3.5 2.3 + - - -
222B ARG 3.4 19.2 - - - +
223B LEU* 4.1 3.1 - - + -
224B PRO* 4.0 27.6 - - + -
371B LEU* 4.2 9.6 - - + -
373B VAL* 4.2 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 217 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B LYS* 2.9 39.4 + - + +
214B ALA* 3.9 6.5 - - - +
216B ILE* 1.3 78.1 - - - +
218B ASP* 1.3 64.4 + - - +
221B GLY* 2.9 27.7 + - - +
222B ARG* 3.7 32.1 - - - +
223B LEU* 4.2 12.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 218 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B ALA 3.0 20.2 + - - +
215B GLN* 3.6 6.1 - - - +
217B LEU* 1.3 80.4 - - - +
219B LYS* 1.3 73.6 + - - +
221B GLY 4.7 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 219 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B LEU* 2.4 41.9 + - + +
60B THR* 4.6 1.4 - - - +
61B LYS* 4.7 1.8 - - - +
74B TYR* 3.8 35.0 + - + +
215B GLN* 2.9 28.6 + - + +
216B ILE* 4.3 1.3 - - - +
218B ASP* 1.3 90.2 - - - +
220B GLU* 1.3 66.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 220 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B LYS* 4.3 6.2 + - - +
72B THR* 4.0 10.7 + - - +
74B TYR* 2.3 47.9 + - + +
216B ILE* 2.9 19.0 + - + +
219B LYS* 1.3 81.4 - - - +
221B GLY* 1.3 62.3 + - - +
222B ARG* 3.5 11.4 + - + +
371B LEU* 4.0 27.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 221 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B ILE 3.5 0.2 + - - -
217B LEU* 2.9 24.8 + - - +
218B ASP 4.7 0.4 + - - -
219B LYS 3.8 0.4 - - - -
220B GLU* 1.3 76.8 - - - +
222B ARG* 1.4 60.2 + - - +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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