Contacts of the helix formed by residues 139 - 150 (chain F) 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 F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104F ALA 2.7 13.6 + - - +
137F ALA 3.5 4.4 + - - +
138F ALA* 1.3 73.9 - - - +
140F PRO* 1.3 66.0 - - - +
141F GLU* 4.1 7.1 + - - +
142F ARG* 3.4 53.2 + - + +
143F VAL* 3.1 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 140 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104F ALA* 4.3 8.0 - - + -
130F LEU* 4.0 15.5 - - + +
133F ILE* 3.9 25.6 - - + +
138F ALA* 3.6 8.7 - - + +
139F ASP* 1.3 86.9 - - - +
141F GLU* 1.3 65.4 + - - +
143F VAL* 3.1 4.5 + - + +
144F ALA* 2.8 34.9 + - - +
160F ARG* 3.5 29.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 141 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139F ASP* 3.5 7.0 + - - +
140F PRO* 1.3 89.7 - - - +
142F ARG* 1.3 60.0 + - - +
144F ALA* 3.5 8.4 - - - +
145F GLU* 3.4 26.0 + - - +
160F ARG* 3.5 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 142 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105F GLY 5.5 7.0 + - - -
106F GLN 4.6 12.9 + - - -
137F ALA 5.7 1.8 + - - -
139F ASP* 3.4 43.7 + - - +
140F PRO 3.2 0.6 - - - -
141F GLU* 1.3 77.2 - - - +
143F VAL* 1.3 72.3 + - - +
145F GLU* 3.1 26.4 + - + +
146F GLU* 3.1 36.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 143 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102F VAL* 3.7 29.6 - - + -
103F ASP 3.8 7.0 - - - +
104F ALA* 3.3 23.3 - - - +
105F GLY 5.4 0.4 - - - -
106F GLN 4.8 1.3 - - - -
107F GLY* 4.1 17.5 - - - +
108F VAL 5.2 0.2 - - - +
130F LEU* 3.8 17.5 - - + -
139F ASP* 3.1 19.6 + - + +
140F PRO 3.8 2.9 - - - +
142F ARG* 1.3 82.7 - - - +
144F ALA* 1.3 64.5 + - - +
146F GLU* 3.1 10.3 + - + +
147F ILE* 3.0 25.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 144 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130F LEU* 4.5 14.5 - - + +
140F PRO 2.8 17.2 + - - +
141F GLU* 3.5 10.3 - - - +
143F VAL* 1.3 77.0 - - - +
145F GLU* 1.3 60.7 + - + +
147F ILE* 3.6 4.0 + - - +
148F GLU* 3.2 24.3 + - - +
155F ALA* 4.0 30.1 - - + +
156F THR* 6.0 0.7 - - - -
160F ARG* 5.9 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 145 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141F GLU 3.4 13.5 + - - +
142F ARG* 3.1 18.1 + - + +
144F ALA* 1.3 78.9 - - - +
146F GLU* 1.3 57.4 + - + +
148F GLU* 3.3 8.7 + - - +
149F ASP* 2.8 31.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 146 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106F GLN 4.7 1.4 - - - +
107F GLY* 3.5 27.7 - - - -
108F VAL* 3.7 11.1 + - + +
142F ARG* 3.1 38.2 + - - +
143F VAL* 3.1 14.7 + - + +
145F GLU* 1.3 73.6 - - + +
147F ILE* 1.3 58.8 + - + +
149F ASP* 4.3 5.2 - - - -
150F ILE* 2.8 57.0 + - + +
438F GLN* 4.5 12.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 147 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100F LEU* 4.4 9.2 - - + -
102F VAL* 3.8 33.2 - - + -
108F VAL* 5.1 6.1 - - + -
128F PRO* 4.7 9.9 - - + -
129F VAL 5.3 1.1 - - - +
130F LEU* 3.8 24.0 - - + -
143F VAL* 3.0 23.2 + - + +
144F ALA 3.9 4.0 - - - +
146F GLU* 1.3 73.8 - - + +
148F GLU* 1.3 61.5 + - - +
151F VAL* 3.1 34.8 + - + +
152F GLY 3.2 6.8 + - - -
153F ILE* 3.6 31.1 + - + +
155F ALA* 4.3 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 148 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144F ALA 3.2 17.0 + - - +
145F GLU* 3.6 8.3 - - - +
147F ILE* 1.3 77.5 - - - +
149F ASP* 1.3 60.5 + - - +
152F GLY* 3.7 14.4 - - - -
153F ILE 3.5 15.9 - - - +
154F ASP* 3.7 13.6 - - - +
155F ALA* 3.4 22.5 + - - -
156F THR* 3.8 16.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 149 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145F GLU 2.8 17.9 + - - +
146F GLU* 3.1 6.3 + - - +
148F GLU* 1.3 80.4 - - - +
150F ILE* 1.3 63.9 + - + +
152F GLY* 4.4 2.8 + - - -
434F TYR 4.2 1.4 - - - +
435F HIS* 3.1 47.4 + - + +
436F GLY 4.4 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 150 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108F VAL* 3.8 22.0 - - + -
113F LEU* 3.8 33.4 - - + -
117F TYR* 3.0 23.3 + - - +
146F GLU* 2.8 33.1 + - + +
149F ASP* 1.3 74.6 - - + +
151F VAL* 1.3 62.4 + - - +
409F LEU* 4.8 10.1 - - + -
435F HIS* 3.6 46.0 + - + +
438F GLN* 4.3 20.0 - - - +
----------------------------------------------------------
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