Contacts of the helix formed by residues 114 - 123 (chain X) in PDB entry 2OU0
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 PHE 114 (chain X).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102X MET* 4.0 18.2 - - + -
106X MET* 3.6 20.6 - - - -
110X GLY 3.4 17.0 - - - -
111X VAL* 2.9 19.4 + - + +
113X GLY* 1.3 77.1 - - - +
115X THR* 1.3 53.3 + - - +
116X ASN 3.3 2.5 - - - -
117X SER* 3.1 15.0 + - - -
118X LEU* 2.8 39.1 + - + +
132X ASN* 5.4 1.6 - - - -
133X LEU* 3.8 32.5 - - + -
135X LYS 5.8 0.2 - - - -
136X SER* 3.8 31.2 - - - -
138X TRP* 4.2 13.7 - + + -
303X MR3 6.3 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 115 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83X LYS* 5.4 6.5 - - + +
112X ALA 3.6 12.1 + - - +
113X GLY* 3.1 10.2 + - - -
114X PHE* 1.3 76.5 - - - +
116X ASN* 1.3 61.8 + - - +
118X LEU* 3.6 12.3 + - + +
119X ARG* 3.1 46.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 116 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114X PHE 3.3 0.6 - - - -
115X THR* 1.3 78.3 - - - +
117X SER* 1.3 64.6 - - - +
119X ARG* 3.1 31.4 + - - +
120X MET* 3.2 34.7 + - + +
132X ASN* 3.8 20.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 117 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114X PHE* 3.1 19.2 + - - -
116X ASN* 1.3 70.6 - - - +
118X LEU* 1.3 61.6 + - - +
120X MET* 3.2 8.8 + - - +
121X LEU* 2.8 35.6 + - - +
129X ALA* 4.4 1.9 - - - +
132X ASN* 2.5 31.8 + - - +
133X LEU* 3.3 42.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 118 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83X LYS* 4.6 14.1 - - + +
84X LEU* 3.9 23.8 - - + -
87X VAL* 3.8 18.5 - - + +
111X VAL* 3.9 13.5 - - + +
112X ALA* 3.9 14.4 - - - +
114X PHE* 2.8 22.6 + - + +
115X THR* 3.6 7.2 - - + +
117X SER* 1.3 76.5 - - - +
119X ARG* 1.3 62.1 + - - +
121X LEU* 3.3 8.8 + - + +
122X GLN* 3.0 23.9 + - - +
303X MR3 3.6 43.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 119 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87X VAL* 5.6 0.2 - - - -
115X THR* 3.1 34.4 + - - +
116X ASN* 3.1 32.7 + - - +
117X SER 3.3 0.2 - - - -
118X LEU* 1.3 75.0 - - - +
120X MET* 1.3 59.1 + - + +
122X GLN* 3.2 7.5 + - - +
123X GLN* 3.0 54.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 120 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116X ASN* 3.2 21.4 + - + +
117X SER 3.2 6.9 + - - +
119X ARG* 1.3 79.2 - - + +
121X LEU* 1.3 57.7 + - - +
123X GLN* 3.4 16.9 + - - +
124X LYS 3.1 7.1 + - - -
125X ARG* 3.0 35.7 + - + +
128X GLU* 3.4 42.4 - - + +
129X ALA* 3.6 14.8 - - + +
132X ASN* 3.8 29.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 121 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87X VAL* 4.1 7.6 - - + -
90X SER* 4.6 0.5 + - - -
91X LEU* 4.1 11.0 - - + +
117X SER 2.8 23.7 + - - +
118X LEU* 3.6 8.3 - - + +
119X ARG 3.2 0.2 - - - -
120X MET* 1.3 77.2 - - - +
122X GLN* 1.3 57.4 + - - +
124X LYS* 3.1 15.1 + - - +
126X TRP* 3.5 35.1 - - + -
129X ALA* 3.7 20.2 - - + -
133X LEU* 4.8 8.7 - - + -
153X PHE* 3.6 54.7 - - + -
303X MR3 4.2 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 122 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86X PRO* 3.6 29.1 + - - +
87X VAL* 3.4 27.3 + - + +
90X SER* 3.8 24.1 + - - +
118X LEU 3.0 14.0 + - - +
119X ARG* 3.2 9.1 + - - +
121X LEU* 1.3 76.0 - - - +
123X GLN* 1.3 61.1 + - + +
124X LYS* 3.1 10.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 123 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119X ARG* 3.0 44.1 + - + +
120X MET* 3.4 18.1 - - - +
121X LEU 3.3 0.2 - - - -
122X GLN* 1.3 76.3 - - + +
124X LYS* 1.3 68.8 + - - +
125X ARG* 3.3 48.2 + - - +
----------------------------------------------------------
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