Contacts of the helix formed by residues 217 - 223 (chain A) in PDB entry 1OVM
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 ASP 217 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A ALA* 1.3 73.1 - - - +
218A PHE* 1.3 68.0 + - - +
219A LEU 2.8 12.5 + - - -
220A VAL* 2.7 30.7 - - - +
221A LEU* 4.2 0.7 + - - +
243A MET* 3.0 40.3 + - + +
245A MET* 2.9 24.2 - - - +
246A GLY* 2.8 24.9 + - - -
249A ILE* 5.2 2.5 - - - -
283A VAL 2.9 8.9 + - - -
284A GLY 3.4 14.2 - - - +
285A THR* 4.1 10.8 - - - -
286A ARG 5.0 0.9 + - - -
291A LEU* 3.9 7.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 218 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A ALA 5.0 3.1 - - - -
92A GLU* 3.6 31.4 - - - -
93A HIS* 3.9 7.9 - + - -
217A ASP* 1.3 95.5 - - - +
219A LEU* 1.3 87.9 + - + +
221A LEU* 2.8 27.9 + - - +
222A ARG* 3.0 29.9 + - + +
245A MET* 3.6 49.4 - - + +
246A GLY* 3.3 9.6 - - - -
284A GLY 4.0 4.5 - - - -
286A ARG* 3.7 36.6 - - + -
406A LEU* 5.5 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 219 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A HIS* 3.8 37.7 - - + +
217A ASP 2.8 6.7 + - - -
218A PHE* 1.3 92.0 - - + +
220A VAL* 1.3 59.5 + - - +
222A ARG* 4.3 2.5 - - + -
223A HIS* 3.0 35.0 + - + +
284A GLY* 3.4 26.0 - - - +
286A ARG* 3.3 37.9 - - - +
308A GLN* 3.4 10.5 - - - +
309A PRO* 3.8 18.4 - - + -
324A MET* 4.0 7.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 220 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A ALA* 4.1 10.5 - - + -
217A ASP 2.7 23.1 - - - +
219A LEU* 1.3 75.2 - - - +
221A LEU* 1.3 63.9 + - - +
223A HIS 3.5 0.7 + - - -
224A GLY 3.3 2.8 + - - -
225A LEU* 2.9 63.4 + - + +
226A LYS* 3.9 8.0 + - - +
229A LEU* 4.2 17.7 - - + -
249A ILE* 4.4 13.0 - - + -
283A VAL* 3.8 26.7 - - + +
284A GLY* 4.5 0.4 - - - -
324A MET* 4.5 5.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 221 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A PHE* 2.8 16.2 + - - +
220A VAL* 1.3 79.2 - - - +
222A ARG* 1.3 78.4 + - - +
224A GLY* 3.3 12.4 + - - -
226A LYS* 4.4 20.4 - - + +
245A MET 4.1 20.4 - - - +
246A GLY* 4.2 9.0 - - - +
247A LYS 4.6 5.4 - - - +
248A GLY 4.9 1.3 - - - -
249A ILE* 3.5 35.0 - - + +
400A ASN* 5.9 4.3 - - - +
401A PHE 5.3 5.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 222 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A ARG* 3.1 52.5 - - - +
92A GLU* 2.7 29.6 + - - +
93A HIS* 2.9 33.0 + - + +
94A VAL* 3.8 8.9 - - - +
95A PRO* 5.2 3.1 - - - -
160A ARG* 3.2 34.5 + - + +
218A PHE* 3.0 32.5 + - + +
219A LEU* 3.8 7.9 - - + +
220A VAL 3.3 0.2 - - - -
221A LEU* 1.3 103.5 - - - +
223A HIS* 1.3 66.9 + - - +
224A GLY 3.3 2.9 + - - -
245A MET* 4.8 1.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 223 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A HIS* 5.3 1.3 - + - -
158A ARG 3.9 10.7 + - - -
159A GLU 4.8 4.0 - - - -
160A ARG* 3.8 33.8 - - + +
187A GLN* 4.4 19.1 - - - -
219A LEU* 3.0 33.8 + - + +
220A VAL 3.5 0.4 + - - +
221A LEU 3.3 0.4 - - - -
222A ARG* 1.3 79.0 - - + +
224A GLY* 1.3 63.9 + - - +
225A LEU* 3.3 25.4 + - + +
309A PRO* 3.8 36.9 - - + +
310A HIS* 5.2 2.9 - + - -
324A MET* 4.3 11.4 - - + -
----------------------------------------------------------
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