Contacts of the helix formed by residues 145 - 156 (chain B) in PDB entry 3C5C
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 THR 145 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B TYR* 4.8 0.3 + - - -
142B ARG* 4.0 13.0 - - + +
144B VAL* 1.3 80.7 - - - +
146B LYS* 1.3 65.3 + - - +
147B ALA* 3.6 11.0 + - - +
148B GLU* 2.7 48.8 + - - +
149B GLY* 3.2 9.5 + - - -
162B GLU* 4.2 1.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 146 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B ARG* 3.7 8.1 - - - +
145B THR* 1.3 72.5 - - - +
147B ALA* 1.3 58.6 + - - +
149B GLY* 2.9 18.4 + - - -
150B VAL* 3.0 25.6 + - + +
160B PHE* 3.5 18.6 - - + -
162B GLU* 3.4 31.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 147 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B THR* 3.2 9.7 + - - +
146B LYS* 1.3 78.5 - - - +
148B GLU* 1.3 58.8 + - + +
150B VAL* 3.2 11.8 + - - +
151B ALA* 2.9 29.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 148 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B ARG* 2.9 34.0 + - - -
106B PHE* 3.4 16.6 - - + -
143B GLN 4.6 0.5 - - - +
144B VAL* 3.8 9.5 - - + -
145B THR* 2.7 47.1 + - - +
147B ALA* 1.3 76.5 - - + +
149B GLY* 1.3 56.7 + - - +
151B ALA* 3.4 8.5 + - + +
152B LEU 3.0 22.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 149 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B TYR* 3.5 23.6 - - - -
106B PHE* 4.1 7.7 - - - -
131B LEU* 3.6 7.2 - - - +
145B THR 3.2 6.7 + - - -
146B LYS 2.9 8.6 + - - -
148B GLU* 1.3 74.2 - - - +
150B VAL* 1.3 58.1 + - - +
152B LEU 3.3 0.7 + - - -
153B ALA* 2.9 28.9 + - - +
160B PHE* 3.6 12.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 150 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B LYS* 3.0 30.7 + - + +
147B ALA* 3.4 10.8 - - - +
149B GLY* 1.3 75.3 - - - +
151B ALA* 1.3 56.9 + - - +
153B ALA* 3.3 5.3 + - - +
154B GLY* 2.9 26.2 + - - -
160B PHE* 3.8 22.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 151 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B ALA 2.9 16.6 + - - +
148B GLU* 3.6 9.9 - - + +
150B VAL* 1.3 75.0 - - - +
152B LEU* 1.3 65.3 + - - +
154B GLY* 3.3 4.2 + - - -
155B ARG* 3.2 26.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 152 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B PHE* 3.4 33.0 - - + +
109B SER* 3.4 25.8 - - - +
110B SER* 3.8 11.9 - - - +
113B LEU* 4.1 8.3 - - + -
131B LEU* 3.8 14.1 - - + -
148B GLU 3.0 16.9 + - - +
149B GLY 3.3 4.5 + - - +
151B ALA* 1.3 74.9 - - - +
153B ALA* 1.3 64.5 + - - +
155B ARG* 3.0 50.6 + - - +
156B PHE* 3.5 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 153 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B LEU* 3.9 4.2 - - + +
149B GLY 2.9 14.4 + - - +
150B VAL 3.5 8.3 - - - +
152B LEU* 1.3 76.4 - - - +
154B GLY* 1.3 51.5 + - - +
156B PHE 3.0 3.1 + - - -
157B GLY* 2.8 31.7 + - - -
158B CYS* 3.1 45.8 + - - +
160B PHE* 3.9 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 154 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B VAL 2.9 14.6 + - - -
151B ALA* 3.6 6.5 - - - -
152B LEU 3.2 0.8 - - - -
153B ALA* 1.3 76.7 - - - +
155B ARG* 1.3 60.0 + - - +
156B PHE 3.3 0.7 + - - -
157B GLY* 3.7 8.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 155 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B PHE* 6.1 1.4 - - - -
110B SER* 4.4 13.1 + - - -
114B GLU* 4.4 8.5 + - - +
151B ALA 3.2 15.1 + - - +
152B LEU* 3.0 36.8 + - - +
154B GLY* 1.3 76.7 - - - +
156B PHE* 1.3 85.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 156 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B SER* 3.9 4.5 - - - -
113B LEU* 3.6 46.9 - - + +
114B GLU* 3.4 59.2 - - + -
117B ALA* 4.3 11.2 - - + -
152B LEU* 3.5 32.5 - - + -
153B ALA 3.0 5.1 + - - +
155B ARG* 1.3 102.0 - - + +
157B GLY* 1.3 61.8 + - - +
158B CYS* 3.3 5.2 + - - +
----------------------------------------------------------
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