Contacts of the helix formed by residues 505 - 512 (chain B) in PDB entry 3MBK
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 505 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418B SER* 6.0 0.4 - - - +
503B TRP* 3.4 8.5 - - + +
504B ILE* 1.3 83.6 - - - +
506B PRO* 1.3 76.3 - - + +
507B SER* 3.2 11.2 - - - +
508B GLU* 2.9 48.1 + - + +
509B LEU 2.9 10.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 506 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484B VAL* 4.2 27.8 - - + +
504B ILE 4.3 2.2 - - - +
505B PRO* 1.3 85.5 - - + +
507B SER* 1.3 63.1 + - - +
509B LEU* 3.6 6.0 - - + +
510B ALA* 2.9 25.8 + - - +
516B VAL* 3.7 22.6 - - + +
517B ASP 4.5 2.5 - - - +
518B THR* 3.8 17.0 - - - +
520B TYR 6.2 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 507 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505B PRO* 4.1 14.6 - - - +
506B PRO* 1.3 77.3 - - - +
508B GLU* 1.3 63.9 + - - +
510B ALA* 3.5 3.5 + - - +
511B ALA* 3.1 24.9 + - - +
518B THR* 4.0 16.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 508 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416B GLN 4.5 11.6 - - - +
417B ARG* 5.0 0.3 - - - -
418B SER* 3.6 24.8 + - - -
504B ILE* 3.4 27.3 - - + +
505B PRO* 2.9 26.8 + - + +
507B SER* 1.3 81.7 + - - +
509B LEU* 1.3 64.8 + - - +
511B ALA* 3.3 9.2 + - + +
512B ALA* 3.0 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 509 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459B PRO 5.2 2.5 - - - +
461B LEU* 3.9 25.1 - - + -
464B VAL* 3.8 30.3 - - + -
484B VAL* 4.1 15.0 - - + -
504B ILE* 3.4 44.9 - - + +
505B PRO 2.9 7.2 + - - +
506B PRO* 3.6 18.8 - - + +
508B GLU* 1.3 76.5 - - - +
510B ALA* 1.3 61.7 + - - +
512B ALA* 3.1 13.9 + - + +
513B ASN 3.4 0.3 + - - -
514B LEU* 3.3 30.5 + - + +
516B VAL* 3.9 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 510 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506B PRO 2.9 15.0 + - - +
507B SER 3.7 3.4 - - - +
509B LEU* 1.3 77.8 - - - +
511B ALA* 1.3 56.4 + - - +
513B ASN* 3.0 21.3 + - - +
514B LEU 4.2 3.8 + - - +
515B SER* 5.5 0.7 - - - +
516B VAL* 4.1 19.1 - - + +
518B THR* 3.6 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 511 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507B SER 3.1 17.2 + - - +
508B GLU* 3.3 10.3 + - + +
510B ALA* 1.3 76.1 - - - +
512B ALA* 1.3 56.5 + - - +
513B ASN* 3.2 13.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 512 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415B PRO* 4.0 34.3 - - + +
504B ILE* 6.1 0.9 - - + -
508B GLU 3.0 15.9 + - - +
509B LEU* 3.1 7.3 + - + +
511B ALA* 1.3 74.7 - - - +
513B ASN* 1.3 74.7 + - - +
514B LEU* 3.5 16.8 + - + +
----------------------------------------------------------
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