Contacts of the helix formed by residues 401 - 407 (chain A) in PDB entry 3BMW
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 ASN 401 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397A LEU 2.8 24.6 + - - +
398A ARG 4.2 3.5 - - - +
399A LYS 5.1 0.4 - - - -
400A SER* 1.3 75.5 + - - +
402A PRO* 1.3 62.2 - - - +
403A ALA* 2.9 23.9 + - - +
404A ILE* 3.0 26.7 + - + +
405A ALA 3.4 5.9 + - - -
428A ASN* 3.9 5.9 - - - +
429A VAL 3.3 24.2 + - - -
430A ALA* 4.1 6.1 - - - +
491A GLN* 3.0 34.1 + - - +
492A TYR 4.7 0.2 - - - -
493A VAL* 3.6 12.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 402 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398A ARG 5.3 0.2 - - - +
400A SER 3.7 8.1 - - - +
401A ASN* 1.3 87.4 - - - +
403A ALA* 1.3 55.5 + - - -
405A ALA* 3.8 5.6 - - + +
406A TYR* 2.9 42.4 + - + +
407A GLY 3.6 0.3 + - - -
425A PHE* 3.7 19.6 - - + +
428A ASN* 3.5 34.8 - - - +
493A VAL* 4.4 5.2 - - + -
497A ASN* 5.8 0.2 - - - +
520A ARG* 3.9 40.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 403 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401A ASN* 2.9 15.7 + - - +
402A PRO* 1.3 80.5 - - - +
404A ILE* 1.3 58.3 + - - +
407A GLY* 2.8 23.9 + - - -
423A ARG* 3.4 32.1 + - + +
425A PHE* 3.7 12.9 - - - +
428A ASN 3.4 28.9 - - - +
429A VAL* 3.8 5.8 - - - +
430A ALA* 4.0 1.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 404 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A LEU 3.8 7.6 - - - +
351A THR* 4.1 23.6 - - + +
397A LEU* 3.6 39.5 - - + +
398A ARG* 3.3 45.3 + - + +
401A ASN* 3.0 20.0 + - + +
403A ALA* 1.3 76.0 - - - +
405A ALA* 1.3 64.0 + - - +
423A ARG* 2.8 26.0 + - + +
430A ALA* 3.7 30.3 - - + -
489A VAL* 5.3 1.6 - - + -
491A GLN* 4.9 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 405 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A SER* 3.3 39.0 - - - +
14A THR* 3.8 14.8 - - + -
319A ASN* 4.2 7.4 - - - +
354A GLY 4.6 1.4 + - - +
398A ARG* 3.3 29.5 + - - +
401A ASN 3.4 6.2 + - - +
402A PRO* 3.5 5.6 + - + +
404A ILE* 1.3 81.1 - - - +
406A TYR* 1.3 71.0 + - + +
423A ARG* 4.5 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 406 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ASP* 2.7 31.5 + - - +
11A ASN* 3.0 31.3 + - - -
13A SER* 4.0 15.0 - - - -
14A THR* 3.4 11.2 - - + +
319A ASN* 3.2 20.6 + - - +
402A PRO* 2.9 26.7 + - + +
405A ALA* 1.3 92.3 - - + +
407A GLY* 1.3 66.3 + - - +
423A ARG* 4.0 1.1 - - - -
425A PHE* 3.8 18.9 - + + -
502A GLY* 3.5 34.4 - - - -
503A HIS* 3.8 10.1 - - + -
518A ASP* 3.7 6.2 - - + +
519A GLY* 4.2 8.5 - - - -
520A ARG* 4.1 10.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 407 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A ILE* 6.0 1.0 - - - +
319A ASN* 4.4 4.0 - - - +
353A ARG* 4.7 2.1 - - - +
402A PRO 3.6 1.6 + - - -
403A ALA 2.8 20.2 + - - -
406A TYR* 1.3 81.6 - - - +
408A THR* 1.3 64.5 + - - -
409A THR* 4.4 1.4 + - - -
423A ARG* 2.8 21.7 + - - +
424A LYS 3.1 19.5 - - - -
425A PHE* 4.0 5.6 - - - -
----------------------------------------------------------
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