Contacts of the helix formed by residues 384 - 388 (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 ARG 384 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382B PRO* 4.6 2.1 - - - +
383B PHE* 1.3 87.6 - - + +
385B ARG* 1.3 65.3 + - - +
386B ALA* 3.1 4.7 + - + +
387B GLU* 3.5 8.5 + - - +
388B SER* 4.0 6.1 + - - -
343D GLU 5.8 2.0 - - - +
344D GLU* 3.7 12.7 + - - +
346D LEU 5.5 1.3 - - - +
348D ARG* 3.8 40.6 - - + +
349D GLY 3.3 25.3 + - - -
350D ASN* 4.2 0.4 - - - +
351D ALA 3.4 16.6 + - - +
352D LEU* 3.2 22.4 + - - -
191O ALA 4.3 0.2 - - - -
192O SER* 3.5 21.7 + - - +
132U LEU* 3.1 52.9 - - + +
133U TYR 4.3 6.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 385 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381B ILE* 6.1 0.6 - - - +
382B PRO* 3.9 19.8 + - + +
383B PHE 3.1 16.0 + - - -
384B ARG* 1.3 68.1 - - - +
386B ALA* 1.3 53.5 + - - +
387B GLU 2.6 20.1 + - - -
388B SER* 3.1 19.9 + - - +
189O GLY 4.4 4.4 + - - -
190O LEU 3.9 10.6 + - - -
191O ALA 3.2 18.2 + - - +
192O SER 3.7 2.8 - - - -
193O GLY 2.9 32.3 + - - +
194O TYR 4.6 2.6 + - - -
195O ASP* 3.9 14.3 + - - -
41U ASN* 3.8 11.9 - - - +
43U VAL* 3.6 27.8 - - + -
44U ASP* 2.8 40.9 + - - +
47U LEU* 3.8 20.8 - - + +
51U TYR* 5.4 3.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 386 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384B ARG* 3.1 3.2 + - + +
385B ARG* 1.3 78.0 - - - +
387B GLU* 1.3 64.8 + - + +
191O ALA* 4.2 4.6 + - - +
51U TYR* 5.2 8.2 + - - -
121U LEU* 6.5 0.9 - - - -
130U ASN* 3.2 31.9 + - - +
132U LEU* 3.2 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 387 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384B ARG 3.5 7.1 + - - +
385B ARG 2.6 5.1 + - - -
386B ALA* 1.3 85.5 - - - +
388B SER* 1.3 64.8 + - - +
389B LYS* 3.4 15.3 + - - +
343D GLU* 5.4 4.2 - - - +
344D GLU* 4.1 6.7 - - - +
130U ASN* 4.8 2.1 + - - -
132U LEU* 3.3 32.4 - - + +
133U TYR 5.7 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 388 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382B PRO* 3.5 14.1 - - - +
384B ARG 4.0 0.8 + - - -
385B ARG* 3.1 27.6 + - - -
387B GLU* 1.3 77.0 - - - +
389B LYS* 1.3 60.0 + - - +
391B SER* 3.8 11.7 - - - -
394B GLN* 2.8 32.3 - - - +
344D GLU* 3.6 20.0 - - - -
47U LEU* 3.8 11.3 - - - +
----------------------------------------------------------
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