Contacts of the helix formed by residues 109 - 116 (chain B) in PDB entry 1OP9
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 TRP 109 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B TRP* 4.3 0.9 - + - -
31B LEU* 3.4 41.1 - - + -
35B GLU* 3.3 32.8 - - - +
57B PHE* 2.8 22.5 + - + -
58B GLN 3.9 9.8 + - - -
59B ILE* 3.8 23.6 - - + +
96B ALA* 3.9 15.5 - - + -
99B VAL* 3.6 31.9 - - + -
100B VAL* 3.6 24.9 - - + -
106B ILE* 3.3 24.8 + - + +
107B ARG 3.1 2.6 - - - -
108B ALA* 1.3 78.7 - - + +
110B VAL* 1.3 64.7 + - - +
111B ALA 3.2 0.2 - - - -
112B TRP* 3.0 12.2 + - + +
113B ARG* 3.3 12.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 110 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B GLU* 4.8 0.8 + - - +
108B ALA 3.5 5.3 + - - -
109B TRP* 1.3 70.6 - - - +
111B ALA* 1.3 68.6 + - + +
113B ARG* 3.0 37.8 + - - +
114B ASN* 3.0 37.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 111 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B TRP* 4.5 22.4 - - + +
35B GLU* 3.3 24.6 + - + +
109B TRP 3.2 0.8 - - - -
110B VAL* 1.3 84.8 - - + +
112B TRP* 1.3 56.7 + - - +
114B ASN* 3.3 7.6 + - - +
115B ARG* 2.9 38.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 112 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B ASN* 3.2 41.3 + - - -
31B LEU* 3.7 23.2 - - + +
35B GLU* 4.3 0.8 + - - -
106B ILE* 3.7 57.3 - - + +
107B ARG* 3.9 21.1 - - + -
109B TRP* 3.0 12.0 + - - +
111B ALA* 1.3 77.8 - - - +
113B ARG* 1.3 66.6 + - + +
116B CYS* 3.0 37.6 + - + +
117B GLN* 2.8 68.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 113 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B GLN* 5.2 2.2 + - - -
107B ARG* 3.4 39.7 + - - +
109B TRP 3.3 10.7 + - - +
110B VAL* 3.0 35.2 + - - +
112B TRP* 1.3 80.1 - - + +
114B ASN* 1.3 70.1 + - - +
115B ARG 3.8 0.2 + - - -
117B GLN* 3.6 42.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 114 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B VAL* 3.0 34.4 + - - +
111B ALA* 3.3 6.7 + - - +
113B ARG* 1.3 91.7 + - - +
115B ARG* 1.3 70.8 + - + +
117B GLN 5.8 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 115 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B CYS* 4.0 3.3 - - - -
34B TRP* 3.6 73.8 + - + +
111B ALA* 2.9 16.7 + - + +
114B ASN* 1.3 90.3 + - + +
116B CYS* 1.3 62.9 + - - +
117B GLN 3.9 1.6 - - - -
119B ARG* 3.4 29.6 + - - +
124B TYR* 5.4 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 116 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B ASN* 4.3 6.8 - - - +
30B CYS* 2.0 62.8 - - + -
31B LEU* 3.8 0.7 - - - -
34B TRP* 3.8 6.7 - - - -
112B TRP* 3.0 41.7 + - + +
115B ARG* 1.3 79.5 - - - +
117B GLN* 1.3 70.3 + - - +
118B ASN 3.3 0.5 + - - -
119B ARG* 3.2 23.4 + - - +
121B VAL* 4.2 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