Contacts of the helix formed by residues 377 - 388 (chain M) in PDB entry 5NSS
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 HIS 377 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370M ILE* 6.4 0.2 - - - -
376M MET* 1.3 77.8 - - - +
378M GLU* 1.3 59.7 + - - +
379M SER* 4.2 7.4 - - - +
380M THR* 2.5 40.8 + - + +
381M ILE* 2.9 15.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 378 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367M LEU* 5.1 15.0 - - + -
370M ILE* 6.3 0.7 - - - -
376M MET 3.9 2.0 + - - -
377M HIS* 1.3 73.1 - - - +
379M SER* 1.3 57.5 + - - +
381M ILE* 4.0 6.5 - - - +
382M SER* 2.9 32.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 379 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377M HIS* 3.2 6.9 - - - +
378M GLU* 1.3 78.1 - - - +
380M THR* 1.3 60.0 - - - +
382M SER* 2.9 17.9 + - - -
383M ARG* 2.9 19.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 380 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343M VAL* 5.8 6.5 - - - -
347M ILE* 5.3 0.7 - - - -
376M MET* 4.0 7.6 - - - +
377M HIS* 2.5 42.9 + - + -
379M SER* 1.3 77.5 - - - +
381M ILE* 1.3 57.8 + - - +
383M ARG* 3.2 6.4 + - - +
384M VAL* 2.9 37.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 381 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347M ILE* 4.4 17.6 - - + +
370M ILE* 4.1 25.8 - - + -
376M MET* 5.6 4.3 - - + -
377M HIS 2.9 15.2 + - - +
378M GLU* 4.0 6.3 - - - +
380M THR* 1.3 77.2 + - - +
382M SER* 1.3 58.9 + - - +
384M VAL* 3.3 2.1 + - - +
385M THR* 2.9 31.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 382 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-15I T 5.5 6.7 + - - -
378M GLU 2.9 23.8 + - - -
379M SER* 2.9 18.4 + - - -
381M ILE* 1.3 77.3 - - - +
383M ARG* 1.3 60.9 + - - +
384M VAL 3.5 0.2 + - - -
385M THR* 3.6 8.5 + - - -
386M THR* 3.6 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 383 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379M SER 2.9 18.8 + - - +
380M THR* 3.2 7.8 + - - +
382M SER* 1.3 77.6 + - - +
384M VAL* 1.3 60.4 + - + +
386M THR* 3.2 17.9 + - - -
387M GLN* 4.1 6.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 384 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340M LEU 5.3 1.1 - - - +
343M VAL* 3.3 31.2 - - + +
344M SER* 3.3 35.4 - - - +
347M ILE* 3.6 25.1 - - + -
348M VAL* 3.6 8.3 - - + +
380M THR* 2.9 21.1 + - - +
381M ILE 3.9 0.4 - - - +
383M ARG* 1.3 78.1 - - + +
385M THR* 1.3 64.9 + - - +
386M THR 3.1 2.5 - - - -
387M GLN* 2.9 17.7 + - - +
388M LYS* 3.5 10.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 385 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347M ILE 5.9 1.6 - - - -
348M VAL* 6.4 0.4 - - - +
351M GLN* 5.6 12.6 - - - -
381M ILE 2.9 18.4 + - - -
382M SER* 4.1 7.2 - - - -
383M ARG 3.5 0.4 - - - -
384M VAL* 1.3 78.3 - - - +
386M THR* 1.3 62.9 + - - +
388M LYS 4.0 12.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 386 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-15I T 4.9 13.7 - - - +
382M SER 3.6 14.4 + - - +
383M ARG* 3.2 14.7 + - - -
385M THR* 1.3 78.7 - - - +
387M GLN* 1.3 68.3 + - - +
388M LYS 5.0 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 387 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344M SER* 5.3 10.3 - - - -
383M ARG 4.3 8.1 - - - +
384M VAL* 2.9 14.7 + - - +
386M THR* 1.3 83.5 + - - +
388M LYS* 1.3 60.2 + - + +
389M TYR 3.7 2.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 388 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344M SER* 4.9 6.5 - - - +
348M VAL* 4.0 26.5 - - + -
384M VAL* 3.5 7.7 + - + +
385M THR* 4.0 11.6 - - - +
386M THR 5.0 1.3 - - - +
387M GLN* 1.3 77.9 - - + +
389M TYR* 1.3 67.0 + - - +
390M LEU* 4.0 1.2 + - - +
----------------------------------------------------------
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