Contacts of the helix formed by residues 209 - 220 (chain B) in PDB entry 5MQF
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 VAL 209 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B GLY 3.7 2.3 + - - -
208B HIS* 1.3 70.5 - - - +
210B ASN* 1.3 60.2 + - - +
212B SER* 2.9 22.0 + - - -
213B ASP* 2.9 12.2 + - - +
632B THR* 5.2 10.8 - - - +
633B GLY* 5.9 2.9 - - - +
899B SER 4.0 20.9 - - - +
900B VAL* 4.9 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 210 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B HIS* 4.8 0.6 - - - +
209B VAL* 1.3 79.6 - - - +
211B PHE* 1.3 57.4 + - - +
213B ASP* 3.0 11.2 + - + +
214B GLU* 2.9 27.7 + - - +
616B SER* 4.4 12.5 - - - -
632B THR* 3.7 29.4 - - - +
633B GLY* 4.3 5.5 - - - +
635B LEU* 6.4 0.4 - - + -
636B TYR* 4.2 26.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 211 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B GLY 5.3 3.8 - - - +
182B LYS* 4.3 8.4 - - + +
206B PRO* 3.3 31.0 - - + +
208B HIS* 3.3 25.9 + - + +
209B VAL 3.2 0.4 - - - -
210B ASN* 1.3 78.5 - - - +
212B SER* 1.3 56.5 + - - +
214B GLU* 3.5 7.8 + - - +
215B VAL* 2.9 26.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 212 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B PRO 4.2 10.0 + - - -
207B GLY* 4.7 4.3 - - - -
208B HIS 2.4 30.4 + - - -
209B VAL* 2.9 7.8 + - - -
211B PHE* 1.3 68.2 - - - +
213B ASP* 1.3 61.3 + - - +
215B VAL* 3.2 9.5 + - - +
216B THR* 2.9 27.0 + - - -
238B ASN* 5.4 10.1 - - - -
242B LEU* 6.5 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 213 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B VAL 2.9 10.7 + - - +
210B ASN* 3.0 13.9 + - - +
212B SER* 1.3 77.0 - - - +
214B GLU* 1.3 56.4 + - - +
216B THR* 3.1 7.3 + - - +
217B ALA* 2.9 26.2 + - - +
582B PHE* 3.4 43.1 - - + +
584B THR* 4.6 9.9 - - - -
616B SER* 5.4 3.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 214 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B LYS* 4.0 28.0 - - + +
183B SER* 5.1 0.3 - - - -
210B ASN 2.9 12.2 + - - +
211B PHE* 3.8 8.1 - - - +
213B ASP* 1.3 75.9 - - - +
215B VAL* 1.3 57.3 + - - +
217B ALA* 3.3 9.5 + - - +
218B GLY* 2.9 24.9 + - - -
615B PRO* 6.3 2.5 - - + -
616B SER* 4.3 18.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 215 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B THR* 5.6 2.6 - - - -
135B CYS* 5.9 1.1 - - + -
182B LYS 4.1 5.8 + - - -
183B SER* 4.3 6.2 - - - -
205B THR* 3.8 29.1 - - - -
206B PRO* 4.0 7.2 - - + +
211B PHE 2.9 19.3 + - - +
212B SER* 3.4 12.6 - - - +
213B ASP 3.2 0.4 - - - -
214B GLU* 1.3 76.4 - - - +
216B THR* 1.3 57.9 + - - +
218B GLY* 3.6 2.0 + - - -
219B LEU* 2.9 26.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 216 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B SER 2.9 13.1 + - - -
213B ASP* 3.1 10.5 + - - -
215B VAL* 1.3 76.5 - - - +
217B ALA* 1.3 60.4 + - - +
218B GLY 3.2 0.2 - - - -
219B LEU* 2.9 9.5 + - - +
220B ARG* 2.9 27.9 + - - +
245B HIS* 5.0 16.4 - - - -
580B LEU* 4.7 1.2 - - - +
581B LYS 4.8 11.2 - - - -
582B PHE 5.4 2.5 - - - -
583B ASN* 6.3 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 217 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B ASP 2.9 12.9 + - - +
214B GLU* 3.3 13.2 + - - +
216B THR* 1.3 75.8 - - - +
218B GLY* 1.3 60.0 + - - +
220B ARG* 3.5 14.0 + - - +
221B ILE* 4.5 2.1 + - - +
479B THR* 5.1 7.4 - - - +
480B LYS* 6.5 0.2 - - - -
580B LEU* 3.8 25.3 - - + +
581B LYS 5.0 2.8 + - - +
582B PHE* 5.8 3.4 - - + -
615B PRO* 6.5 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 218 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B SER* 6.1 3.1 - - - -
214B GLU 2.9 15.3 + - - -
215B VAL* 3.7 2.9 - - - -
217B ALA* 1.3 77.0 - - - +
219B LEU* 1.3 61.6 + - - +
220B ARG 3.2 0.2 - - - -
221B ILE* 3.5 19.3 + - - +
222B SER* 4.4 2.3 + - - -
479B THR* 5.3 7.9 - - - -
480B LYS* 6.0 4.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 219 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B THR* 5.0 17.9 - - - -
215B VAL 2.9 18.6 + - - +
216B THR* 2.9 13.4 + - - +
218B GLY* 1.3 72.5 - - - +
220B ARG* 1.3 60.3 + - - +
221B ILE 3.1 5.8 + - - -
222B SER* 3.1 23.2 + - - +
224B GLY 5.2 1.7 - - - +
225B VAL* 5.5 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 220 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B THR 2.9 7.4 + - - +
217B ALA 3.6 4.9 - - - +
218B GLY 3.2 1.0 - - - -
219B LEU* 1.3 74.7 - - - +
221B ILE* 1.3 62.6 + - - +
222B SER 4.1 2.3 - - - +
249B GLU* 6.5 1.3 - - - -
580B LEU* 3.6 31.2 - - + -
----------------------------------------------------------
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