Contacts of the helix formed by residues 376 - 389 (chain O) in PDB entry 5MQF
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 VAL 376 (chain O).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375O ASP* 1.3 71.8 - - - +
377O LYS* 1.3 59.7 + - - +
379O TRP* 3.3 6.7 + - - +
380O ILE* 2.9 30.2 + - - +
413O GLU* 4.6 6.7 - - + +
414O HIS* 4.0 35.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 377 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128N ALA 4.5 12.3 - - - +
130N ALA* 3.7 27.9 - - + +
375O ASP* 3.3 5.9 - - + +
376O VAL* 1.3 79.9 - - - +
378O ASN* 1.3 56.8 + - - +
380O ILE* 3.4 6.7 + - - +
381O LYS* 2.9 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 378 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130N ALA* 5.1 1.5 - - - +
370O VAL* 4.0 28.2 - - + +
373O HIS 4.4 9.4 - - - +
374O PRO* 5.0 0.2 - - + -
375O ASP* 3.5 20.3 + - + +
376O VAL 3.3 0.2 - - - -
377O LYS* 1.3 77.4 - - - +
379O TRP* 1.3 60.4 + - - +
381O LYS* 3.3 6.0 + - - +
382O TYR* 2.9 31.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 379 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375O ASP 3.2 16.1 + - - +
376O VAL* 3.3 8.0 + - - +
378O ASN* 1.3 75.9 - - - +
380O ILE* 1.3 58.3 + - - +
382O TYR* 4.1 4.3 - - - +
383O ALA* 2.9 31.0 + - - +
399O TYR* 6.3 2.5 - - - -
402O ALA* 5.1 15.7 - - + -
414O HIS 5.9 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 380 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376O VAL 2.9 17.2 + - - +
377O LYS* 3.8 7.0 - - - +
378O ASN 3.3 0.2 - - - -
379O TRP* 1.3 75.6 - - - +
381O LYS* 1.3 59.5 + - - +
383O ALA* 3.8 5.0 - - - +
384O ARG* 2.9 29.8 + - - +
417O VAL* 6.6 0.4 - - + -
418O ALA* 6.4 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 381 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130N ALA* 5.1 5.2 - - + -
131N GLN* 4.5 27.6 - - + +
347O HIS* 6.4 0.7 - - + -
377O LYS 2.9 18.7 + - - +
378O ASN* 3.3 6.9 + - - +
379O TRP 3.3 0.2 - - - -
380O ILE* 1.3 75.8 - - - +
382O TYR* 1.3 59.6 + - - +
384O ARG* 3.2 5.7 + - - +
385O PHE* 2.9 31.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 382 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366O TYR* 5.7 11.9 - - + +
370O VAL* 5.6 7.2 - - + -
378O ASN 2.9 18.7 + - - +
379O TRP* 4.1 4.3 - - - +
381O LYS* 1.3 76.1 - - - +
383O ALA* 1.3 57.2 + - - +
385O PHE* 4.3 4.4 - - - +
386O GLU* 2.9 32.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 383 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379O TRP 2.9 20.6 + - - +
380O ILE* 3.8 7.0 - - - +
382O TYR* 1.3 76.3 - - - +
384O ARG* 1.3 59.7 + - - +
386O GLU* 3.8 4.1 - - - +
387O GLU* 2.9 27.7 + - - +
395O ALA* 5.1 12.8 - - + +
399O TYR* 6.0 4.0 - - + -
418O ALA* 5.5 11.0 - - + -
421O LYS* 6.2 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 384 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131N GLN 5.9 1.8 - - - +
132N LEU* 6.0 6.3 - - + -
380O ILE 2.9 17.9 + - - +
381O LYS* 3.2 6.5 + - - +
383O ALA* 1.3 75.7 - - - +
385O PHE* 1.3 60.8 + - - +
387O GLU* 3.1 7.6 + - - +
388O LYS* 2.9 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 385 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381O LYS 2.9 15.5 + - - +
382O TYR* 4.3 4.7 - - - +
384O ARG* 1.3 75.4 - - - +
386O GLU* 1.3 58.5 + - - +
388O LYS* 3.3 8.2 + - - +
389O HIS* 2.9 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 386 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382O TYR 2.9 22.2 + - - +
383O ALA 4.2 0.9 - - - +
385O PHE* 1.3 77.2 - - - +
387O GLU* 1.3 58.9 + - - +
389O HIS* 3.3 14.2 + - - +
390O ALA 2.8 24.4 - - - +
391O TYR* 4.7 2.5 - - + +
392O PHE* 4.5 2.9 + - - +
395O ALA* 3.7 29.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 387 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383O ALA 2.9 21.9 + - - +
384O ARG* 3.1 9.8 + - - +
386O GLU* 1.3 77.9 - - - +
388O LYS* 1.3 60.9 + - - +
389O HIS 3.3 0.7 + - - -
390O ALA* 3.5 12.9 + - - +
392O PHE* 5.9 3.8 - - - -
395O ALA* 6.0 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 388 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384O ARG 2.9 14.4 + - - +
385O PHE* 3.3 7.2 + - - +
387O GLU* 1.3 75.3 - - - +
389O HIS* 1.3 55.8 + - - +
390O ALA 3.3 2.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 389 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359O VAL* 6.2 4.3 - - + -
385O PHE 2.9 16.7 + - - +
386O GLU* 3.5 12.8 - - - +
387O GLU 3.1 0.8 - - - -
388O LYS* 1.3 77.4 - - - +
390O ALA* 1.3 68.6 + - - +
391O TYR* 3.5 8.7 + - + +
----------------------------------------------------------
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