Contacts of the helix formed by residues 54 - 59 (chain B) in PDB entry 2AXT
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 54 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B PHE* 6.0 0.4 - - + -
49B ASP 3.5 3.8 - - - +
50B PRO* 4.1 19.7 - - + +
51B VAL 4.1 7.6 - - - +
52B LEU* 3.3 8.5 - - - +
53B ASN* 1.3 96.8 - - - +
55B MET* 1.3 69.5 + - + +
56B TRP* 3.0 46.0 + - + +
57B ARG* 3.0 24.0 + - + +
58B GLN* 3.8 3.5 + - - -
266B GLU 4.8 4.0 - - - +
308B LYS* 6.0 2.7 - - - -
311B PHE* 4.5 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 55 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B PHE* 3.7 27.8 - - + -
53B ASN 4.0 0.2 + - - -
54B PRO* 1.3 70.6 - - + +
56B TRP* 1.3 63.7 + - - +
58B GLN* 3.1 13.0 + - - +
60B MET* 3.2 30.3 + - + +
63B LEU* 3.7 24.2 - - + +
64B PRO* 3.7 21.3 - - + -
67B ALA* 4.3 7.2 - - + -
80B ILE* 3.1 43.5 - - + -
93B PHE* 5.2 0.2 - - + -
266B GLU 4.1 10.8 - - - +
267B LEU* 3.6 31.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 56 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B PRO* 3.1 31.7 - - + +
55B MET* 1.3 76.2 - - - +
57B ARG* 1.3 67.9 + - - +
58B GLN 3.3 0.2 - - - -
59B GLY 3.9 4.8 + - - -
60B MET 5.0 0.7 - - - -
265B ILE 3.9 6.8 + - - -
266B GLU* 3.5 25.7 + - - +
267B LEU 4.0 9.2 - - - +
268B PHE 3.9 7.4 - - - -
269B GLY* 3.7 30.7 - - - +
270B PRO* 3.6 17.5 - - + -
311B PHE* 4.4 8.1 - + - -
312B TYR* 3.9 23.2 + + - -
317B ASN* 3.0 44.4 - - + -
330B MET* 3.9 22.0 - - - +
446B SER* 4.7 1.3 - - - -
447B PRO* 3.4 32.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 57 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B LEU 4.3 5.8 + - - +
53B ASN* 4.0 5.4 - - - +
54B PRO* 3.0 35.2 + - + +
56B TRP* 1.3 85.4 - - + +
58B GLN* 1.3 57.7 + - - +
59B GLY 3.2 2.7 - - - -
311B PHE* 4.0 18.0 - - + -
314B TYR* 4.5 1.8 - - - -
316B GLY 3.7 15.0 + - - -
317B ASN* 2.8 31.1 + - - -
329B PRO* 3.3 0.7 - - - +
330B MET* 2.9 44.5 + - - +
331B ASN* 3.2 30.9 + - - +
334B ASP* 2.8 32.7 + - - -
335B GLY 2.9 18.6 + - - -
337B ALA* 4.5 2.4 - - - +
432B PHE* 4.2 6.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 58 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B THR 4.0 4.2 - - - +
45B PHE* 3.4 21.7 - - - -
46B ASP* 2.8 48.8 + - - +
53B ASN* 3.2 38.2 + - - +
54B PRO 3.8 5.5 + - - +
55B MET 3.1 7.2 + - - +
57B ARG* 1.3 79.6 - - - +
59B GLY* 1.3 63.8 + - - -
60B MET* 3.0 17.3 - - + +
329B PRO* 3.2 11.9 - - - -
331B ASN* 3.9 9.0 - - - +
517B CLA 2.9 13.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 59 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B GLU* 4.3 1.2 - - - +
56B TRP 3.9 7.2 + - - -
57B ARG 3.2 2.8 - - - -
58B GLN* 1.3 77.4 - - - +
60B MET* 1.3 62.7 + - - +
61B PHE 3.7 1.4 + - - -
329B PRO* 3.2 14.0 - - - +
330B MET* 4.4 0.8 - - - +
447B PRO* 4.7 3.1 - - - -
517B CLA 3.0 56.2 - - - +
----------------------------------------------------------
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