Contacts of the helix formed by residues 139 - 151 (chain A) in PDB entry 3CB4
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 ASP 139 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A ALA 2.8 11.5 + - - +
137A ALA 3.3 6.9 + - - +
138A ALA* 1.3 72.9 - - - +
140A PRO* 1.3 66.4 - - - +
141A GLU* 4.1 5.4 + - - +
142A ARG* 3.3 51.8 + - - +
143A VAL* 3.2 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 140 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A ALA* 4.5 8.3 - - + -
130A LEU* 4.0 15.5 - - + +
133A ILE* 4.1 22.0 - - + -
138A ALA* 3.7 8.5 - - + +
139A ASP* 1.3 88.9 - - - +
141A GLU* 1.3 66.8 + - - +
143A VAL* 3.3 3.6 + - + +
144A ALA* 2.8 30.4 + - - +
160A ARG* 3.2 30.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 141 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A ASP* 3.5 4.8 + - - +
140A PRO* 1.3 88.7 - - - +
142A ARG* 1.3 62.3 + - - +
144A ALA* 3.2 9.4 + - - +
145A GLU* 3.2 25.9 + - - +
160A ARG* 3.3 32.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A GLY 5.1 7.9 + - - -
106A GLN 3.5 19.8 + - - -
137A ALA 5.5 1.4 + - - -
139A ASP* 3.3 41.4 + - - +
140A PRO 3.4 0.4 - - - -
141A GLU* 1.3 77.6 - - - +
143A VAL* 1.3 74.2 + - - +
145A GLU* 3.3 18.7 + - + +
146A GLU* 3.1 48.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 143 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A VAL* 3.7 29.8 - - + -
103A ASP 4.0 3.8 - - - +
104A ALA* 3.5 19.5 - - - +
106A GLN 4.5 0.4 - - - -
107A GLY* 4.0 15.3 - - - +
130A LEU* 3.8 17.0 - - + -
139A ASP 3.2 18.3 + - - +
140A PRO 3.8 3.8 - - - +
142A ARG* 1.3 96.5 - - - +
144A ALA* 1.3 63.3 + - - +
145A GLU 3.2 0.7 - - - -
146A GLU* 3.3 7.7 + - + +
147A ILE* 3.1 25.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 144 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A LEU* 4.7 8.0 - - + +
140A PRO 2.8 13.9 + - - +
141A GLU* 3.2 14.6 + - + +
143A VAL* 1.3 78.3 - - - +
145A GLU* 1.3 62.3 + - - +
147A ILE* 3.7 2.6 + - - -
148A GLU* 3.3 25.3 + - - +
155A ALA* 3.8 33.5 - - + +
156A THR* 5.4 4.3 - - + -
160A ARG* 6.0 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 145 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A GLU 3.2 14.1 + - - +
142A ARG* 3.3 19.5 - - + +
143A VAL 3.2 0.4 - - - -
144A ALA* 1.3 75.1 - - - +
146A GLU* 1.3 54.4 + - + +
148A GLU* 3.2 6.9 + - - +
149A ASP* 2.8 40.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 146 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A GLN 4.6 1.2 - - - +
107A GLY* 3.4 5.3 - - - -
108A VAL* 3.2 38.3 + - + +
142A ARG* 3.1 45.3 + - - +
143A VAL* 3.3 11.4 + - + +
145A GLU* 1.3 77.0 - - + +
147A ILE* 1.3 60.9 + - + +
149A ASP* 4.6 4.0 - - - -
150A ILE* 3.1 44.0 + - + +
438A GLN* 5.2 8.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 147 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A LEU* 4.2 16.4 - - + -
102A VAL* 3.9 29.2 - - + -
108A VAL* 5.4 6.3 - - + -
128A PRO* 4.5 11.4 - - + -
129A VAL 5.3 0.9 - - - +
130A LEU* 3.8 24.9 - - + -
143A VAL* 3.1 19.1 + - + +
144A ALA 4.0 4.0 - - - +
145A GLU 3.3 0.2 - - - -
146A GLU* 1.3 74.8 - - + +
148A GLU* 1.3 60.2 + - - +
151A VAL* 3.0 32.7 + - + +
152A GLY 3.1 5.9 + - - -
153A ILE* 3.9 29.6 + - + -
155A ALA* 4.0 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 148 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A ALA* 3.3 16.6 + - - +
145A GLU* 3.2 8.6 + - - +
147A ILE* 1.3 80.5 - - - +
149A ASP* 1.3 59.6 + - - +
152A GLY* 3.3 20.2 - - - -
153A ILE 3.7 16.1 + - - +
154A ASP* 4.4 5.3 - - - -
155A ALA 3.4 22.9 + - - -
156A THR* 3.6 23.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 149 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A GLU* 2.8 22.9 + - + +
146A GLU* 4.1 4.0 - - - +
148A GLU* 1.3 76.2 - - - +
150A ILE* 1.3 61.5 + - + +
152A GLY* 4.7 0.9 + - - -
434A TYR 4.4 1.6 - - - +
435A HIS* 3.1 45.3 + - - +
436A GLY 4.4 1.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 150 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A VAL* 3.8 20.6 - - + -
113A LEU* 3.8 34.3 - - + -
117A TYR* 3.2 16.9 + - - +
146A GLU* 3.1 28.2 + - + +
149A ASP* 1.3 80.2 - - + +
151A VAL* 1.3 62.0 + - + +
409A LEU* 4.8 7.4 - - + -
435A HIS* 3.5 49.2 + - + +
438A GLN* 4.4 15.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 151 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A LEU* 4.4 15.9 - - + -
108A VAL* 4.5 9.0 - - + -
113A LEU* 3.5 28.9 - - + -
116A CYS* 3.8 26.9 - - + -
117A TYR* 4.4 6.0 - - + -
120A MET* 3.6 33.7 - - + +
147A ILE* 3.0 18.8 + - + +
150A ILE* 1.3 77.8 - - + +
152A GLY* 1.3 62.0 + - - +
153A ILE* 4.3 14.4 - - + +
----------------------------------------------------------
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