Contacts of the helix formed by residues 202 - 208 (chain M) in PDB entry 5GJQ
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 ILE 202 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198M LEU* 3.9 19.7 - - + +
199M VAL 2.8 5.7 + - - +
200M GLU 3.5 0.2 - - - -
201M ALA* 1.3 87.7 - - + +
203M VAL* 1.3 71.5 + - + +
204M LEU 3.3 1.3 - - - -
205M PRO* 3.2 2.6 - - - +
206M MET* 2.9 26.2 + - + +
222M GLY* 6.0 2.2 - - - -
223M VAL* 5.5 2.9 - - + -
240M CYS* 4.8 1.3 - - - -
244M THR* 4.7 2.9 - - + -
282M ILE* 3.0 44.2 - - + -
327M LYS* 3.1 29.0 + - + +
329M ILE* 2.8 43.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 203 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185M TYR* 5.2 4.0 - - - +
199M VAL* 2.9 41.9 + - + +
202M ILE* 1.3 77.4 - - + +
204M LEU* 1.3 61.5 + - + +
206M MET* 2.9 8.2 + - - +
207M ASN* 2.6 50.1 + - + +
240M CYS* 5.4 2.0 - - - -
243M GLN* 5.8 2.5 - - + -
244M THR* 4.0 26.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 204 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352L MET* 5.8 2.9 - - + -
355L ILE* 5.3 12.6 - - + -
199M VAL* 3.7 4.5 + - + -
200M GLU* 3.7 41.1 - - - +
203M VAL* 1.3 87.5 - - + +
205M PRO* 1.4 64.3 - - + +
206M MET 2.9 0.3 + - - -
207M ASN* 4.5 1.3 - - + +
208M HIS* 2.7 68.9 + - + +
211M LYS* 4.8 14.4 - - + +
212M PHE* 4.0 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 205 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200M GLU 3.5 13.2 - - - +
201M ALA* 3.5 23.3 - - - +
202M ILE 3.2 13.7 - - - +
204M LEU* 1.4 94.8 - - + +
206M MET* 1.3 55.1 + - - +
208M HIS 4.0 0.2 - - - -
209M LYS* 3.1 26.3 - - - +
212M PHE* 3.3 26.4 - - + -
219M PRO* 3.8 28.6 - - + +
220M PRO* 4.9 4.0 - - + +
327M LYS* 4.4 9.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 206 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202M ILE* 2.9 12.6 + - + +
203M VAL* 3.2 5.2 - - - +
204M LEU 2.9 0.6 + - - -
205M PRO* 1.3 75.8 - - - +
207M ASN* 1.3 79.6 + - - +
208M HIS 3.1 8.6 + - - -
209M LYS* 3.4 29.7 - - - +
246M ALA* 5.4 2.7 - - + -
280M PRO* 3.7 36.3 - - + -
327M LYS* 2.8 26.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 207 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203M VAL* 2.6 34.1 + - + +
204M LEU* 3.5 0.9 - - + -
206M MET* 1.3 96.7 - - - +
208M HIS* 1.3 84.2 + - + +
209M LYS* 5.7 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 208 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204M LEU* 2.7 43.2 + - + +
205M PRO* 3.8 0.9 - - - +
206M MET 3.1 2.8 + - - -
207M ASN* 1.3 92.7 + - + +
209M LYS* 1.3 55.5 + - - +
210M GLU* 3.4 7.0 - - - +
211M LYS* 4.1 34.6 + - + +
212M PHE* 2.8 37.6 - - + -
----------------------------------------------------------
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