Contacts of the helix formed by residues 110 - 116 (chain C) in PDB entry 3OMA
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 110 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C HEA 3.9 27.8 - - + -
37C GLY* 3.6 20.3 - - - +
40C VAL* 3.6 9.0 - - + +
41C GLY* 3.5 33.7 - - - +
105C LEU* 3.0 23.1 + - + +
106C MET* 3.9 14.6 - - - +
109C PHE* 1.3 82.8 - - - +
111C VAL* 1.3 67.7 + - + +
113C PRO* 3.5 6.6 - - - +
114C ALA* 3.0 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 111 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C HEA 3.5 26.9 - - + -
106C MET 3.4 13.5 + - - +
110C VAL* 1.3 85.7 - - + +
112C ILE* 1.3 64.1 + - + +
114C ALA* 3.4 4.9 + - - +
115C LEU* 3.0 35.3 + - + +
290C ILE* 3.4 43.5 - - + -
428C ALA* 4.9 3.1 - - + -
429C VAL* 4.2 12.8 - - + -
432C ILE* 3.9 19.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 112 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C MET 4.9 0.6 + - - -
107C MET 3.8 8.7 + - - +
108C PHE* 5.4 1.3 - - - +
111C VAL* 1.3 73.7 - - + +
113C PRO* 1.4 67.4 - - + +
115C LEU* 4.5 2.5 - - - +
116C PHE* 2.8 56.3 + - + +
201C SER* 4.8 12.6 - - - +
239C ILE* 5.0 2.5 - - + -
286C GLU* 3.4 37.9 - - - +
289C ILE* 3.7 30.7 - - + +
290C ILE* 3.7 23.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 113 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C TYR* 3.4 31.6 - - + +
108C PHE 3.5 26.7 - - - +
109C PHE 3.7 4.5 - - - -
110C VAL 3.5 15.3 - - - +
111C VAL 3.7 0.4 - - - +
112C ILE* 1.4 93.4 - - + +
114C ALA* 1.3 56.1 + - - +
117C GLY* 3.4 2.9 - - - +
118C GLY 2.8 23.9 + - - -
146C TYR* 3.6 39.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 114 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C HEA 3.9 29.2 - - + -
33C TYR 4.6 6.5 - - - -
34C LEU* 3.9 12.2 - - + +
37C GLY* 4.9 2.7 - - - -
110C VAL 3.0 19.8 + - - +
111C VAL 3.6 5.6 - - - +
112C ILE 3.1 0.4 - - - -
113C PRO* 1.3 76.9 - - - +
115C LEU* 1.3 58.1 + - - +
118C GLY* 3.2 20.8 - - - -
119C PHE* 3.2 8.1 + - - -
432C ILE* 3.9 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 115 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111C VAL* 3.0 22.0 + - + +
112C ILE* 4.4 2.5 - - - +
114C ALA* 1.3 75.9 - - - +
116C PHE* 1.3 61.9 + - + +
119C PHE* 3.5 10.8 + - + +
120C GLY* 3.0 21.0 + - - -
228C PHE* 4.3 1.7 - - - -
232C ILE* 4.0 6.2 - - - +
290C ILE* 3.5 24.2 - - - +
293C PRO* 3.9 13.7 - - + +
294C ALA* 4.3 14.8 - - + +
297C ILE* 3.6 29.8 - - + -
428C ALA* 4.2 15.9 - - + +
432C ILE* 3.5 38.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 116 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112C ILE* 2.8 32.4 + - + +
115C LEU* 1.3 73.6 - - - +
117C GLY* 1.3 63.5 + - - +
120C GLY* 3.1 24.4 - - - -
121C ASN 3.3 3.5 + - - -
201C SER* 4.2 6.5 - - - -
204C GLY* 3.9 22.9 - - - -
205C ALA* 3.9 9.9 - - - -
208C MET* 3.4 31.0 - - + +
232C ILE* 3.7 42.2 - - + -
235C THR* 3.6 25.6 - - + -
236C ALA* 4.1 4.0 - - + -
239C ILE* 3.6 25.8 - - + -
293C PRO* 4.8 4.9 - - + -
----------------------------------------------------------
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