Contacts of the helix formed by residues 151 - 157 (chain A) in PDB entry 3CMT
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 PRO 151 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A GLU* 3.5 13.5 - - - +
149A LEU 3.3 10.1 - - - +
150A THR* 1.3 87.6 - - - +
152A LYS* 1.3 65.6 + - - +
153A ALA 3.3 0.4 - - - +
154A GLU* 3.1 40.7 + - + +
155A ILE* 3.2 10.2 + - - +
166A LEU* 3.7 26.7 - - + -
167A ALA* 3.8 35.7 - - + +
170A MET* 4.4 6.3 - - - -
1176A ARG* 4.9 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 152 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A THR* 3.9 29.2 - - + +
123A GLU* 2.7 27.0 + - + +
151A PRO* 1.3 72.0 - - - +
153A ALA* 1.3 62.4 + - - +
155A ILE* 3.3 4.6 + - - +
156A GLU* 3.2 48.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 153 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A GLU* 5.3 0.2 + - - -
151A PRO* 3.3 0.6 - - - +
152A LYS* 1.3 77.7 - - - +
154A GLU* 1.3 61.4 + - - +
156A GLU* 4.0 9.1 - - - +
157A GLY* 3.1 18.0 + - - -
163A HIS* 3.4 16.0 - - + -
166A LEU* 4.0 27.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 154 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A THR* 3.6 13.2 - - + +
151A PRO* 3.1 34.3 + - + +
153A ALA* 1.3 80.0 - - - +
155A ILE* 1.3 57.1 + - - +
157A GLY 3.1 21.8 + - - +
158A GLU 4.8 0.9 - - - +
163A HIS* 3.5 33.7 + - + +
1173A GLN* 3.1 33.1 - - + +
1176A ARG* 2.8 38.3 + - - -
1177A LYS* 3.4 11.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 155 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A ASP* 3.3 27.1 - - + +
121A THR* 3.8 15.0 - - + -
150A THR* 3.4 45.3 - - + +
151A PRO 3.2 4.0 + - - +
152A LYS* 3.3 6.3 + - - +
154A GLU* 1.3 76.5 - - - +
156A GLU* 1.3 64.1 + - + +
1130A ASP* 5.2 0.7 - - - +
1134A ARG* 5.6 1.9 + - - -
1176A ARG 5.6 0.7 - - - +
1177A LYS* 3.4 32.4 + - + +
1181A ASN* 5.6 10.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 156 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A LYS* 3.2 48.0 + - + +
153A ALA* 4.0 7.1 - - - +
155A ILE* 1.3 78.8 - - + +
157A GLY* 1.3 60.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 157 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A ALA 3.1 16.4 + - - -
154A GLU 3.1 7.6 + - - +
155A ILE 3.4 0.2 - - - -
156A GLU* 1.3 79.4 - - - +
158A GLU* 1.3 57.4 + - - -
161A ASP* 3.5 8.5 - - - -
163A HIS* 4.7 4.5 - - - -
1177A LYS* 2.7 31.2 + - - -
----------------------------------------------------------
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