Contacts of the helix formed by residues 141 - 146 (chain A) in PDB entry 5B82
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 CYS 141 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A VAL* 4.2 11.0 - - + -
138A GLN* 3.3 31.2 - - - +
139A ALA 3.2 0.4 - - - -
140A SER* 1.3 77.5 + - - +
142A LEU* 1.3 56.0 + - - +
143A ALA 2.9 3.6 + - - -
144A CYS* 3.0 4.2 + - - -
145A HIS* 2.9 33.8 + - + +
173A ARG* 6.3 0.4 - - - -
501A HEC 1.7 89.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A GLY* 4.5 18.4 - - - +
137A VAL* 3.9 16.2 - - + -
138A GLN 4.0 5.2 - - - +
139A ALA* 3.3 16.2 - - + +
140A SER 3.1 0.8 + - - -
141A CYS* 1.3 76.9 - - - +
143A ALA* 1.3 62.2 + - - +
144A CYS 3.1 0.7 - - - -
145A HIS 4.5 0.4 - - - +
146A GLY* 3.1 31.5 + - - +
147A ALA 4.6 0.9 + - - -
150A ARG* 6.0 1.9 - - - +
167A PHE* 3.2 36.1 - - + +
168A ARG* 4.2 2.2 - - - -
169A VAL* 3.9 25.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 143 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A LEU* 4.4 13.2 - - + -
53A GLU 4.0 15.7 + - - +
54A GLY* 5.5 1.6 - - - -
56A THR 6.0 2.2 - - - -
63A THR* 4.6 14.2 - - + +
139A ALA 4.3 0.8 + - - -
140A SER 2.9 16.7 + - - +
142A LEU* 1.3 79.4 - - - +
144A CYS* 1.3 62.0 + - - +
150A ARG 3.9 9.5 - - - +
152A PRO* 3.7 16.8 - - - +
501A HEC 4.2 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 144 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A THR* 4.4 2.7 - - - -
94A ARG* 2.9 29.3 + - - +
141A CYS 3.0 2.2 + - - -
143A ALA* 1.3 83.9 - - - +
145A HIS* 1.3 62.5 + - - +
146A GLY 3.6 2.0 - - - -
151A ARG* 4.0 12.4 - - - +
152A PRO* 3.8 25.7 - - + +
155A ILE* 5.1 1.6 - - + -
501A HEC 1.8 72.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 145 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A ARG* 3.3 18.5 + - - -
137A VAL* 6.1 0.7 - - + -
141A CYS* 2.9 13.5 + - + +
142A LEU* 4.2 2.7 - - + -
144A CYS* 1.3 75.1 - - - +
146A GLY* 1.3 65.0 + - - +
164A ALA* 2.8 29.8 + - + +
165A TYR* 3.4 2.4 - - - +
166A GLY 3.3 2.8 + - - -
167A PHE* 3.3 35.5 + - + +
173A ARG* 3.2 25.5 + - - +
501A HEC 2.1 84.1 + + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 146 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A LEU* 3.1 38.3 + - - -
144A CYS 3.6 1.6 - - - -
145A HIS* 1.3 77.7 - - - +
147A ALA* 1.3 66.4 + - - +
165A TYR* 3.4 3.3 - - - +
166A GLY* 2.7 30.7 + - - -
167A PHE 4.4 3.1 - - - -
----------------------------------------------------------
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