Contacts of the helix formed by residues 105 - 112 (chain A) in PDB entry 2O07
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 105 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A GLY 2.9 14.4 + - - -
103A GLY 3.2 1.0 - - - -
104A ASP* 1.3 75.8 + - - +
106A GLY* 1.3 57.6 + - - +
107A VAL 3.4 2.5 - - - -
108A LEU* 3.3 12.9 - - - +
109A ARG 2.9 23.0 + - - -
140A MET 3.1 14.7 - - - +
143A GLY* 3.6 4.0 - - - -
144A TYR* 3.6 21.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 106 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A GLN* 3.4 17.7 - - - +
104A ASP* 3.0 14.9 + - - -
105A GLY* 1.3 74.9 - - - +
107A VAL* 1.3 64.5 + - - +
109A ARG* 3.3 10.8 + - - +
110A GLU* 3.1 25.6 + - - +
140A MET* 3.5 19.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 107 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A GLN* 3.5 18.3 + - + +
83A ILE* 3.4 29.2 - - + -
84A ALA* 4.6 2.5 - - + -
99A ILE* 3.8 22.7 - - + -
102A GLY* 5.4 2.4 + - - -
104A ASP* 4.3 1.0 + - - -
105A GLY 3.4 0.4 - - - -
106A GLY* 1.3 71.9 - - - +
108A LEU* 1.3 62.4 + - - +
110A GLU* 3.0 7.5 + - - +
111A VAL* 2.8 36.4 + - + +
171A ILE* 4.0 23.8 - - + -
173A ASP* 3.4 28.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 108 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A ILE* 3.6 9.5 - - + +
102A GLY 5.8 0.2 + - - -
105A GLY 3.3 9.4 - - - +
107A VAL* 1.3 76.2 - - - +
109A ARG* 1.3 62.9 + - - +
111A VAL* 3.2 2.4 + - - -
112A VAL* 3.1 39.1 + - + +
120A VAL* 3.7 35.7 - - + -
122A GLN* 4.0 16.4 + - - +
143A GLY* 3.3 32.1 - - - +
144A TYR* 3.8 16.6 - - + +
146A SER* 5.2 0.2 - - - -
149A LEU* 3.9 37.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 109 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A GLU* 2.9 42.9 + - - -
77A PHE* 4.5 6.5 - - - +
80A GLN* 3.5 16.6 - - - +
105A GLY 2.9 17.4 + - - +
106A GLY* 3.3 12.5 + - - +
108A LEU* 1.3 73.3 - - - +
110A GLU* 1.3 86.1 + - - +
112A VAL* 3.6 12.5 - - - +
113A LYS* 3.5 26.2 - - - +
139A GLY 2.9 29.1 + - - -
140A MET* 3.6 11.4 - - - +
142A ILE* 3.7 16.4 - - + -
143A GLY* 3.7 15.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 110 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A GLN 3.6 22.7 - - - +
81A GLU* 3.7 23.9 - - - +
84A ALA* 3.6 21.5 - - + +
85A ASN* 4.5 4.9 - - - +
106A GLY 3.1 12.0 + - - +
107A VAL 3.0 5.1 + - - +
109A ARG* 1.3 104.3 + - - +
111A VAL* 1.3 67.5 + - - +
113A LYS* 3.0 49.3 + - - +
114A HIS* 3.9 9.5 + - - -
276A LEU* 3.7 6.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 111 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A ALA* 3.9 5.4 - - + -
88A LEU* 3.8 17.3 - - + -
97A VAL* 4.0 11.4 - - + -
99A ILE* 4.1 7.9 - - + -
107A VAL* 2.8 27.6 + - + +
108A LEU* 3.8 4.7 - - - +
110A GLU* 1.3 72.6 - - - +
112A VAL* 1.3 57.9 + - - +
113A LYS 3.1 0.2 - - - -
114A HIS* 3.1 28.4 + - - +
117A VAL* 3.9 19.0 - - + +
120A VAL* 3.6 29.4 - - + -
171A ILE* 3.8 29.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 112 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A LEU* 3.1 34.2 + - + +
109A ARG* 3.6 15.0 - - - +
111A VAL* 1.3 73.4 - - - +
113A LYS* 1.3 61.2 + - + +
114A HIS 3.1 0.7 - - - -
117A VAL* 5.2 0.4 - - - -
120A VAL* 4.1 9.9 - - + -
143A GLY* 5.2 2.2 - - - +
146A SER* 3.4 37.0 - - - +
148A LYS* 2.8 43.0 + - + +
----------------------------------------------------------
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