Contacts of the helix formed by residues 380 - 389 (chain A) in PDB entry 1MUK
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 THR 380 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A TYR* 5.7 3.4 - - + -
81A VAL 5.5 1.0 + - - -
92A VAL 5.4 0.4 + - - -
135A THR* 4.0 15.3 - - + -
139A ILE* 3.7 26.0 - - + -
379A ARG* 1.3 77.8 - - - +
381A PRO* 1.3 71.1 - - - +
382A THR* 3.8 3.5 + - - -
383A GLU* 3.0 39.1 + - + +
384A THR* 3.2 11.0 + - - -
665A ASP* 3.4 15.4 + - - -
667A PHE* 4.4 4.0 - - + -
668A SER* 3.5 15.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 381 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A ARG 4.1 2.0 - - - +
380A THR* 1.3 81.4 - - - +
382A THR* 1.3 62.3 + - - +
384A THR* 3.0 4.1 + - - +
385A VAL* 2.8 29.8 + - - +
515A MET* 4.8 3.4 - - - -
517A LEU* 4.0 35.7 - - + -
663A VAL* 4.6 8.5 - - + -
664A ASN 5.3 2.0 - - - +
665A ASP* 3.2 35.2 - - + +
666A SER 5.1 1.1 - - - +
667A PHE* 3.8 20.6 - - + -
806A ALA 5.7 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 382 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A ARG* 4.4 4.3 - - - -
81A VAL 4.3 2.7 - - - +
82A ARG* 3.7 28.0 - - - -
380A THR* 3.9 4.9 - - - -
381A PRO* 1.3 77.3 - - - +
383A GLU* 1.3 57.7 + - - +
385A VAL* 3.4 1.7 + - - +
386A LEU* 3.0 36.1 + - + +
663A VAL* 4.6 0.9 - - - +
665A ASP* 2.5 33.0 + - - +
671A ASN* 3.2 26.3 + - - +
673A PHE* 4.0 24.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 383 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A VAL 4.7 0.9 - - - +
82A ARG* 3.5 25.5 + - - -
83A ARG* 2.7 37.8 + - + +
92A VAL* 3.1 53.1 - - + +
379A ARG* 3.9 7.3 + - + -
380A THR* 3.0 25.5 + - + +
382A THR* 1.3 78.6 - - - +
384A THR* 1.3 64.5 + - - +
386A LEU* 3.4 4.6 + - - +
387A GLN* 3.1 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 384 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A ARG* 2.7 43.8 + - - +
380A THR 3.2 4.1 + - - -
381A PRO* 3.0 11.0 + - - -
383A GLU* 1.3 78.4 - - - +
385A VAL* 1.3 65.5 + - - +
387A GLN 3.2 0.2 + - - -
388A GLU* 3.0 29.6 + - + +
515A MET* 4.8 0.4 - - + -
517A LEU* 4.4 13.6 - - + +
525A PRO* 3.6 22.5 - - + +
527A SER* 3.4 24.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 385 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381A PRO 2.8 23.9 + - - +
382A THR* 3.7 5.2 - - - +
384A THR* 1.3 73.8 - - - +
386A LEU* 1.3 62.7 + - + +
389A TYR* 3.2 39.8 + - + +
515A MET* 3.1 33.7 - - + -
661A TYR* 5.5 2.5 - - + -
663A VAL* 3.6 33.0 - - + -
673A PHE* 4.3 6.7 - - + -
675A HIS* 4.1 25.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 386 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A ARG* 3.6 28.5 - - - +
82A ARG* 3.1 55.9 - - - +
382A THR* 3.0 23.2 + - + +
383A GLU* 4.1 4.9 - - - +
385A VAL* 1.3 76.4 - - + +
387A GLN* 1.3 57.0 + - - +
390A THR* 3.2 30.7 + - - +
673A PHE* 4.5 8.1 - - + -
675A HIS* 4.0 26.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 387 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A PRO* 3.4 28.7 - - + +
90A ASP* 3.4 20.2 + - - +
92A VAL* 5.9 5.6 - - + -
93A TYR* 5.2 0.6 + - - -
379A ARG* 2.9 28.5 - - - +
383A GLU 3.1 16.5 + - - +
384A THR 4.1 0.9 - - - +
385A VAL 3.2 0.2 - - - -
386A LEU* 1.3 80.3 - - - +
388A GLU* 1.3 79.8 + - - +
389A TYR 3.5 1.0 + - - -
390A THR* 4.4 8.8 + - - +
391A GLN* 5.4 1.0 + - - +
524A ARG* 4.7 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 388 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A ARG* 3.1 12.4 + - - +
384A THR* 3.0 25.2 + - + +
387A GLN* 1.3 107.5 + - - +
389A TYR* 1.3 79.3 + - + +
390A THR 3.8 0.9 - - - -
524A ARG* 2.6 38.2 + - - -
525A PRO 4.8 3.4 - - - +
527A SER* 4.6 4.0 - - - +
591A ALA* 4.8 6.1 - - - +
679A THR* 3.8 12.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 389 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A VAL* 3.2 34.0 + - + +
388A GLU* 1.3 86.9 - - + +
390A THR* 1.3 61.6 + - - +
391A GLN 3.8 2.0 - - - -
515A MET* 3.3 25.1 - - + -
527A SER* 2.7 34.3 + - - -
529A MET* 3.5 14.5 - - + +
661A TYR* 3.4 33.7 - + - -
675A HIS* 3.1 27.4 - - + +
677A THR* 2.8 21.2 + - + +
679A THR* 3.4 40.2 - - + -
680A PHE 5.0 2.2 - - - -
682A SER* 5.3 1.0 + - - -
----------------------------------------------------------
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