Contacts of the helix formed by residues 399 - 416 (chain G) in PDB entry 1MKD
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 399 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398G ASP* 1.3 101.9 - - - +
400G TYR* 1.3 62.0 + - - +
401G SER* 2.6 47.1 + - - +
402G ASP* 3.2 24.3 + - - +
403G ARG* 3.0 28.7 + - - +
398L ASP* 3.4 29.9 + - + +
399L ASN* 4.0 11.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 400 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286G GLU* 5.2 8.1 - - - -
359G LYS* 3.7 29.7 - - + +
360G MET* 3.8 31.1 - - + +
363G ASP* 2.9 24.1 + - - -
399G ASN* 1.3 69.9 - - - +
401G SER* 1.3 59.2 + - - +
402G ASP 2.9 4.3 - - - -
403G ARG* 2.7 25.3 + - + +
404G ILE* 2.7 66.3 + - + +
398L ASP* 5.8 2.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 401 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399G ASN* 2.6 22.6 + - - +
400G TYR* 1.3 83.9 - - - +
402G ASP* 1.3 61.2 + - - +
404G ILE* 3.5 14.6 - - - +
405G GLN* 3.2 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 402 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383G MET* 3.2 26.4 - - + +
388G LYS* 5.0 2.9 + - - -
396G LEU 5.1 0.2 - - - +
397G LEU* 4.1 18.0 - - + +
398G ASP* 3.5 17.2 - - - +
399G ASN* 3.2 27.4 + - - +
400G TYR 2.8 0.8 + - - -
401G SER* 1.3 83.7 + - - +
403G ARG* 1.3 66.4 + - - +
405G GLN* 3.4 5.4 + - - +
406G VAL* 3.2 28.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 403 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281G VAL* 3.7 23.5 + - - -
282G PHE* 3.7 13.2 - - + -
283G THR* 5.2 5.2 - - - +
286G GLU* 2.8 36.5 + - - +
397G LEU* 3.4 37.9 + - + -
398G ASP 2.9 28.3 + - - -
399G ASN 3.0 15.8 + - - +
400G TYR* 2.7 29.5 + - + +
402G ASP* 1.3 71.8 - - - +
404G ILE* 1.3 59.4 + - - +
405G GLN 3.1 1.8 - - - -
406G VAL* 3.2 3.5 + - - +
407G LEU* 3.0 32.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 404 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360G MET* 3.9 37.2 - - + +
363G ASP* 4.1 14.8 - - + +
364G ILE* 4.2 13.2 - - + -
400G TYR* 2.7 58.2 + - + +
401G SER* 3.5 17.7 - - - +
403G ARG* 1.3 72.9 - - - +
405G GLN* 1.3 61.8 + - + +
407G LEU* 4.4 8.5 - - + -
408G GLN* 2.9 36.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 405 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376G LEU* 5.2 1.6 - - + -
379G ASP* 3.7 44.9 + - + +
380G LEU* 5.1 0.8 - - + -
383G MET* 3.1 30.3 - - + +
401G SER* 3.2 20.2 + - - +
402G ASP* 3.4 7.3 + - - +
404G ILE* 1.3 81.0 - - - +
406G VAL* 1.3 64.9 + - - +
408G GLN* 3.4 16.1 + - - +
409G ASN* 2.9 41.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 406 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278G LEU* 4.6 6.3 - - + -
282G PHE* 3.8 22.4 - - + -
380G LEU* 5.4 2.7 - - + -
383G MET* 3.7 21.1 - - - -
395G LEU* 5.7 0.9 - - + -
397G LEU* 3.6 19.5 - - + -
402G ASP 3.2 14.8 - - - +
403G ARG 3.2 6.7 + - - +
405G GLN* 1.3 74.5 - - - +
407G LEU* 1.3 58.6 + - - +
409G ASN* 3.4 4.4 + - - +
410G MET* 2.8 28.7 + - + +
481G TRP* 3.8 25.9 - - + -
484G LEU* 4.3 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 407 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273G LEU* 4.1 12.3 - - + -
282G PHE* 3.6 31.9 - - + -
286G GLU* 4.0 34.8 - - + +
290G ALA* 4.0 18.4 - - + -
360G MET* 5.0 3.8 - - - -
364G ILE* 4.0 23.3 - - + +
403G ARG* 3.0 20.0 + - + +
404G ILE* 3.9 15.3 - - + +
406G VAL* 1.3 73.8 - - - +
408G GLN* 1.3 65.2 + - - +
410G MET* 3.5 8.6 - - - +
411G VAL* 3.0 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 408 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363G ASP* 3.0 38.4 - - - +
364G ILE* 3.9 15.7 - - + +
367G ALA* 3.7 20.2 - - + +
368G THR* 6.1 0.3 - - - +
376G LEU* 4.1 16.6 - - + +
404G ILE* 2.9 32.2 + - + +
405G GLN* 3.5 19.4 + - - +
407G LEU* 1.3 79.0 - - - +
409G ASN* 1.3 63.6 + - - +
411G VAL* 3.3 2.3 + - - +
412G HIS* 3.0 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 409 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376G LEU* 3.2 46.1 + - - +
380G LEU* 3.7 44.0 - - + +
405G GLN* 2.9 31.5 + - - +
406G VAL 3.9 3.4 - - - +
408G GLN* 1.3 79.4 - - - +
410G MET* 1.3 57.4 + - - +
412G HIS* 3.3 7.4 + - - +
413G CYS* 2.8 34.4 + - - -
477G LEU* 4.3 10.4 - - + +
481G TRP* 4.4 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 410 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269G THR* 4.3 11.4 - - + +
272G LEU* 3.7 30.2 - - + +
273G LEU* 3.5 43.7 - - + -
278G LEU* 3.4 32.8 - - + -
282G PHE* 4.3 7.2 - - + -
290G ALA* 5.4 0.7 - - - -
406G VAL* 2.8 20.7 + - + +
407G LEU* 3.5 13.9 - - + +
408G GLN 3.1 0.2 - - - -
409G ASN* 1.3 77.9 - - - +
411G VAL* 1.3 58.6 + - - +
413G CYS* 3.0 7.9 + - - +
414G ALA* 2.9 27.1 + - - +
481G TRP* 3.7 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 411 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265G VAL* 4.4 9.0 - - + -
269G THR* 4.0 10.8 - - + +
290G ALA* 4.0 15.3 - - + +
293G ALA 5.3 0.2 - - - -
294G SER* 3.7 32.5 - - - +
297G HIS* 5.3 2.7 - - + -
364G ILE* 3.5 30.1 - - + -
368G THR* 4.3 17.0 - - + -
407G LEU 3.0 15.1 + - - +
408G GLN 4.0 1.1 - - - +
410G MET* 1.3 76.2 - - + +
412G HIS* 1.3 51.4 + - - +
414G ALA* 3.3 6.9 + - - +
415G ASP* 2.8 33.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 412 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367G ALA 3.9 15.8 + - - +
368G THR* 4.5 14.0 + - - +
369G ASP 5.2 0.4 - - - -
370G MET* 3.9 16.2 - - - -
373G HIS* 2.9 36.0 + - + +
376G LEU* 4.0 19.1 - - + -
408G GLN 3.0 17.6 + - - +
409G ASN* 3.4 9.0 - - - +
410G MET 3.1 0.2 - - - -
411G VAL* 1.3 78.0 - - - +
413G CYS* 1.3 57.5 + - - +
415G ASP* 3.3 10.1 + - - +
416G LEU* 3.0 50.9 + - + +
477G LEU* 3.4 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 413 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272G LEU* 4.2 5.4 - - + -
409G ASN* 2.8 20.0 + - - +
410G MET* 3.0 8.9 + - - +
412G HIS* 1.3 73.7 - - - +
414G ALA* 1.3 65.3 + - - +
416G LEU 3.1 4.0 + - - -
417G SER 3.0 18.5 + - - -
477G LEU* 3.7 32.5 - - - -
478G TRP* 3.3 33.2 - - + +
481G TRP* 3.8 35.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 414 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264G ASP* 5.4 0.9 - - - +
265G VAL* 3.8 24.1 - - + +
268G SER* 3.9 13.5 - - - -
269G THR* 3.4 29.2 - - - +
272G LEU* 4.2 5.6 - - + +
410G MET 2.9 11.6 + - - +
411G VAL 3.5 7.0 - - - +
412G HIS 3.3 0.2 - - - -
413G CYS* 1.3 74.7 - - - +
415G ASP* 1.3 61.5 + - - +
417G SER* 2.8 27.7 + - - -
418G ASN* 5.5 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 415 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256G TYR* 4.3 7.3 + - - -
261G HIS* 3.0 18.7 + - - -
265G VAL* 3.9 8.9 - - + +
297G HIS* 2.8 18.4 + - + +
368G THR* 4.1 20.9 - - + +
411G VAL 2.8 18.5 + - - +
412G HIS* 3.6 11.4 + - - +
414G ALA* 1.3 78.0 - - - +
416G LEU* 1.3 68.2 + - + +
417G SER 3.4 1.6 + - - -
418G ASN* 5.2 2.4 + - - +
2013G ZN 2.3 35.1 - - - -
3007G ZAR 6.0 1.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 416 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370G MET* 4.0 14.8 - - + -
412G HIS* 3.0 47.0 + - + +
413G CYS 3.1 5.6 + - - +
415G ASP* 1.3 88.2 - - + +
417G SER* 1.3 57.9 + - - +
418G ASN* 3.6 2.7 - - - -
419G PRO* 4.0 4.5 - - - +
469G PHE* 3.7 26.0 - - + -
473G ILE* 3.9 21.1 - - + -
474G VAL* 3.7 19.5 - - + +
477G LEU* 3.8 17.0 - - + -
478G TRP* 3.2 14.2 + - - -
3007G ZAR 4.8 13.9 - - + -
----------------------------------------------------------
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