Contacts of the helix formed by residues 201 - 210 (chain A) in PDB entry 2M1W
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 201 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A GLU* 6.2 0.2 - - - -
199A SER* 3.2 9.9 + - - -
200A ARG* 1.3 76.7 - - - +
202A PHE* 1.3 63.5 + - - +
203A PRO* 3.1 4.7 - - - -
204A THR* 3.1 15.4 + - - -
205A GLN* 3.0 34.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 202 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A VAL* 5.2 2.5 - - + -
99A LEU* 3.6 42.2 - - + -
100A LEU* 4.8 1.6 - - + -
103A ASP* 5.5 2.0 - - - -
104A PHE* 4.1 11.2 - + - -
173A MET* 5.0 2.7 - - + -
195A LEU* 4.4 3.4 - - + +
196A GLU* 2.8 31.3 - - - +
197A GLU* 3.4 32.3 - - + -
199A SER* 3.2 21.0 + - - +
201A GLY* 1.3 78.0 - - - +
203A PRO* 1.4 69.4 - - + +
205A GLN* 4.4 1.6 - - - +
206A VAL* 2.6 58.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 203 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A ASP* 4.7 3.4 - - - +
104A PHE* 3.6 26.8 - - + -
199A SER 4.5 0.4 - - - +
200A ARG 3.3 14.8 - - - +
201A GLY 3.1 4.9 - - - -
202A PHE* 1.4 108.8 - - + +
204A THR* 1.3 65.2 + - - +
206A VAL* 3.5 1.7 - - - +
207A GLU* 3.0 30.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 204 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A GLY* 3.1 19.7 + - - +
203A PRO* 1.3 78.4 - - - +
205A GLN* 1.3 63.4 + - + +
207A GLU* 2.6 30.1 + - - +
208A ARG* 2.8 45.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 205 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A ASN* 3.1 28.0 + - - +
194A ALA 2.6 31.9 + - - -
195A LEU* 3.5 15.8 - - + +
196A GLU* 4.5 12.2 + - + +
201A GLY* 3.0 17.4 + - - +
202A PHE* 4.4 1.6 - - - +
204A THR* 1.3 82.6 - - + +
206A VAL* 1.3 56.6 + - - +
208A ARG* 4.3 7.0 - - - +
209A ILE* 2.7 43.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 206 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A LEU* 3.4 14.6 - - + -
104A PHE* 2.8 42.0 - - + -
106A ILE* 4.2 2.2 - - + +
195A LEU* 3.4 29.4 - - + -
202A PHE* 2.6 38.6 + - + +
203A PRO 3.5 5.4 - - - +
204A THR 3.0 0.4 - - - -
205A GLN* 1.3 77.0 - - - +
207A GLU* 1.3 58.2 + - - +
210A PHE* 3.1 39.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 207 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A PHE* 3.8 30.0 - - + +
203A PRO* 3.0 21.0 + - + +
204A THR* 2.6 17.1 + - - +
206A VAL* 1.3 72.2 - - - +
208A ARG* 1.3 75.7 + - - +
210A PHE 3.0 3.0 - - - +
211A GLN* 2.7 42.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 208 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A ASN* 6.0 1.1 - - - +
204A THR* 2.8 45.5 + - + +
205A GLN* 3.9 6.5 - - - +
207A GLU* 1.3 103.3 + - - +
209A ILE* 1.3 72.3 + - + +
211A GLN* 3.2 31.9 + - - +
214A VAL* 3.9 4.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 209 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A TRP* 2.6 51.1 + - + +
171A ILE* 3.5 23.6 - - + -
193A ASN* 3.4 32.5 - - - +
195A LEU* 3.0 35.4 - - + -
205A GLN* 2.7 25.2 + - + +
208A ARG* 1.3 78.1 - - + +
210A PHE* 1.3 84.3 + - + +
211A GLN 3.4 1.0 + - - -
214A VAL* 3.5 5.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 210 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A LYS* 4.2 3.2 + - - -
81A PHE* 3.6 23.8 - + - -
100A LEU* 4.2 11.0 - - + -
106A ILE* 3.4 42.7 - - + +
134A TRP* 3.1 49.1 - + + -
136A ILE* 3.9 13.7 - - + -
171A ILE* 4.5 6.1 - - + -
195A LEU* 4.5 9.6 - - + -
206A VAL* 3.1 39.6 + - + +
207A GLU* 3.0 9.6 - - - +
208A ARG 3.2 0.2 - - - -
209A ILE* 1.3 100.5 - - + +
211A GLN* 1.3 58.9 + - - +
212A GLU 4.3 0.5 + - - -
----------------------------------------------------------
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