Contacts of the helix formed by residues 132 - 140 (chain A) in PDB entry 1ODC
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 132 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A TRP* 3.5 19.1 - - - -
130A TYR 2.9 6.0 + - - -
131A ASN* 1.3 73.8 + - - +
133A LYS* 1.3 59.0 + - - +
134A TYR 3.3 1.1 + - - -
135A LEU* 3.4 3.3 + - - -
136A ALA* 2.9 30.5 + - - +
143A LEU* 3.2 32.7 - - - +
448A PHE* 4.2 5.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 133 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A VAL* 4.4 9.7 - - + +
21A PRO* 2.8 34.6 + - - +
22A VAL* 3.6 15.5 - - + +
27A ILE* 3.6 14.5 - - + +
100A TRP* 3.6 21.7 - - + +
131A ASN* 3.2 29.9 + - - +
132A GLY* 1.3 77.9 - - - +
134A TYR* 1.3 96.4 + - + +
137A TYR* 2.9 32.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 134 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A VAL* 3.7 16.2 - - + -
23A LEU* 4.1 21.8 - - + -
131A ASN* 4.1 21.8 + - + -
132A GLY 3.3 0.6 - - - -
133A LYS* 1.3 108.0 + - + +
135A LEU* 1.3 59.1 + - - +
137A TYR* 3.9 0.4 - - - +
138A THR* 2.9 40.3 + - - +
448A PHE 3.4 23.8 - - - +
449A GLY* 4.2 16.6 - - - +
450A LEU* 4.2 20.8 - - + +
452A LEU* 5.2 1.6 - - + -
453A VAL* 3.6 31.1 - - + +
470A MET* 4.5 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 135 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A MET* 4.6 9.9 - - + -
132A GLY* 3.4 8.6 + - - +
133A LYS 3.4 0.2 - - - -
134A TYR* 1.3 78.8 - - - +
136A ALA* 1.3 66.3 + - - +
139A GLU* 3.0 38.7 + - + +
141A VAL* 3.8 8.9 - - + +
143A LEU* 3.9 26.0 - - + -
197A PHE* 4.1 18.4 - - + -
447A VAL* 3.7 18.2 - - + +
448A PHE* 4.3 11.5 + - + +
470A MET* 3.7 44.8 - - + +
473A TRP* 5.6 1.8 - - + -
474A ALA* 5.1 4.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 136 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A ILE* 4.1 6.7 - - + -
100A TRP* 3.7 28.3 - - + +
102A PRO* 3.8 7.8 - - + +
132A GLY 2.9 17.6 + - - +
133A LYS 3.9 2.7 - - - +
135A LEU* 1.3 76.4 - - - +
137A TYR* 1.3 58.6 + - - +
140A GLU* 2.8 31.9 + - - -
141A VAL* 3.2 27.3 + - - +
143A LEU* 4.2 4.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 137 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A VAL* 4.1 22.2 - - + -
23A LEU* 4.1 27.8 + - + -
25A SER* 3.6 33.7 - - - -
26A HIS 4.9 0.9 - - - -
27A ILE* 4.0 26.2 - - + +
102A PRO* 5.5 2.8 - - + +
133A LYS 2.9 19.2 + - - +
134A TYR 3.9 1.1 - - - +
136A ALA* 1.3 80.7 - - - +
138A THR* 1.3 75.3 + - - +
140A GLU* 3.6 12.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 138 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LEU* 4.3 1.0 - - - +
134A TYR 2.9 21.1 + - - -
137A TYR* 1.3 86.9 - - - +
139A GLU* 1.3 76.9 + - - +
140A GLU* 3.8 3.3 + - - +
452A LEU* 3.7 18.2 - - - +
467A ARG* 3.7 26.9 + - + +
470A MET* 4.4 15.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 139 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A LEU* 3.0 26.3 + - + +
138A THR* 1.3 94.0 - - - +
140A GLU* 1.3 73.1 + - - +
141A VAL* 3.3 9.5 + - + +
467A ARG 4.4 1.7 - - - +
470A MET* 3.7 12.1 - - + +
471A HIS* 2.6 56.5 + - - +
474A ALA* 3.5 29.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 140 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A PRO* 3.9 20.8 - - + +
106A PRO* 5.5 1.5 - - + +
109A THR* 3.2 23.5 + - - +
110A THR* 5.2 0.2 - - - -
136A ALA 2.8 14.1 + - - -
137A TYR 3.6 8.2 + - - +
138A THR 3.5 4.8 - - - +
139A GLU* 1.3 82.0 - - - +
141A VAL* 1.3 58.7 + - - +
----------------------------------------------------------
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