Contacts of the helix formed by residues 131 - 137 (chain A) in PDB entry 3A0B
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 TRP 131 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A PHE* 4.7 1.3 - + - -
128A GLY* 2.5 13.4 + - - +
130A GLN* 1.3 82.0 - - - +
132A GLU* 1.3 97.3 + - + -
133A LEU 2.9 6.1 - - - -
134A SER* 2.6 33.1 + - - +
135A TYR* 3.0 26.3 + - + +
136A ARG* 4.3 4.9 - - - -
141A PRO* 3.6 27.1 - - + +
144A CYS* 3.6 22.9 - - + -
446C GLY* 3.9 25.3 + - - -
449C ARG* 4.1 21.5 - - + +
1029C CLA 3.2 52.3 - + + -
23I PHE* 4.0 13.0 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 132 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A THR* 4.4 1.2 - - - +
29A TYR* 2.6 32.4 + - + +
31A GLY* 2.8 27.9 - - - -
32A TRP* 2.5 33.7 + - - +
33A PHE* 3.1 16.4 + - + +
128A GLY 3.4 0.2 + - - -
129A ARG* 3.3 17.4 - - - +
130A GLN 3.7 0.4 - - - -
131A TRP* 1.3 107.8 - - + +
133A LEU* 1.3 56.0 + - - +
135A TYR* 4.2 0.2 - - - +
136A ARG* 2.8 40.1 + - - +
23I PHE* 4.4 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 133 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A THR* 5.7 3.6 - - - -
29A TYR* 3.1 49.3 - - + -
129A ARG 5.1 1.7 + - - +
130A GLN 4.9 1.1 - - - -
131A TRP* 2.9 1.0 - - - +
132A GLU* 1.3 75.7 - - - +
134A SER* 1.3 58.1 + - - +
135A TYR 2.8 5.8 - - - -
136A ARG* 4.0 5.2 - - + +
137A LEU* 2.8 56.4 + - + +
139A MET* 4.1 0.5 - - - +
251D ARG 3.8 0.2 - - - +
252D PHE* 3.3 51.1 - - + +
255D GLN* 3.3 29.2 - - + +
256D ILE* 5.1 4.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 134 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A GLN 3.6 1.9 + - - -
131A TRP* 2.6 36.1 + - - -
133A LEU* 1.3 74.4 - - - +
135A TYR* 1.3 54.2 - - - -
137A LEU 3.2 7.6 - - - +
139A MET* 2.7 38.2 + - - +
140A ARG 4.0 3.7 + - - -
141A PRO* 3.4 36.8 + - - +
143A ILE* 4.3 2.9 - - - +
455C PHE* 3.8 2.8 - - - -
252D PHE* 3.6 13.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 135 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A TRP* 3.0 27.4 + + + +
132A GLU 4.2 1.8 - - - +
133A LEU 2.8 1.0 - - - -
134A SER* 1.3 77.2 - - - +
136A ARG* 1.3 69.1 + - - +
137A LEU 2.5 18.2 + - - -
265C ILE* 4.3 1.7 - - - +
449C ARG* 2.8 71.0 + - + -
452C ALA 4.7 1.9 + - - -
453C ALA* 3.5 15.4 - - + +
455C PHE* 3.1 38.8 - + - -
27I ASP 3.7 11.0 - - - -
28I PRO 2.7 27.7 + - - -
30I ARG 3.4 19.1 - - - -
31I ASN* 3.5 12.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 136 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A THR* 4.0 28.1 - - - +
24A THR* 3.4 16.4 - - + +
29A TYR* 3.3 27.0 + - + +
32A TRP* 4.1 7.1 - - - +
131A TRP* 4.3 4.8 - - - -
132A GLU* 2.8 35.8 + - - +
133A LEU* 4.0 6.5 - - + -
135A TYR* 1.3 94.2 - - - +
137A LEU* 1.3 71.1 + - + +
138A GLY 4.2 0.2 - - - -
449C ARG* 3.9 2.6 - - - +
23I PHE* 3.7 17.4 - - - -
26I GLY 4.8 0.4 + - - -
27I ASP* 2.5 32.3 + - - +
30I ARG* 3.2 44.0 + - + +
31I ASN* 4.3 10.9 - - - +
32I PRO* 4.6 1.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 137 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A THR* 3.5 27.8 - - + -
133A LEU* 2.8 54.1 + - + +
134A SER 3.2 1.9 - - - +
135A TYR 2.5 6.0 + - - -
136A ARG* 1.3 93.5 - - + +
138A GLY* 1.3 68.2 + - - +
139A MET* 3.0 14.7 + - + +
465C PRO* 5.4 5.8 - - + -
466C VAL* 4.6 20.9 - - + -
469C MET* 4.0 18.2 - - + -
248D THR 5.1 3.6 - - - +
251D ARG* 4.9 2.2 - - + +
252D PHE* 4.8 10.3 - - + +
255D GLN* 4.1 8.3 - - - +
32I PRO* 4.5 1.3 - - - -
----------------------------------------------------------
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