Contacts of the helix formed by residues 399 - 416 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398D ASP* 1.3 97.5 - - - +
400D TYR* 1.3 62.1 + - - +
401D SER* 2.6 45.9 + - - +
402D ASP* 3.2 23.8 + - - +
403D ARG* 3.1 29.1 + - - +
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Residues in contact with TYR 400 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286D GLU* 5.2 7.4 - - - -
359D LYS* 3.7 28.7 - - + +
360D MET* 3.8 31.0 - - + +
363D ASP* 2.9 24.6 + - - -
399D ASN* 1.3 70.3 - - - +
401D SER* 1.3 58.3 + - - +
402D ASP 2.9 4.9 - - - -
403D ARG* 2.7 24.2 + - + +
404D ILE* 2.7 66.9 + - + +
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Residues in contact with SER 401 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399D ASN* 2.6 21.5 + - - +
400D TYR* 1.3 84.6 - - - +
402D ASP* 1.3 60.5 + - - +
404D ILE* 3.5 14.0 - - - +
405D GLN* 3.2 31.8 + - - +
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Residues in contact with ASP 402 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383D MET* 3.2 25.9 - - + +
388D LYS* 5.0 3.5 + - - -
396D LEU 5.0 0.2 - - - +
397D LEU* 4.1 18.3 - - + +
398D ASP* 3.5 17.2 - - - +
399D ASN* 3.2 27.8 - - - +
400D TYR 2.9 0.6 - - - -
401D SER* 1.3 83.3 + - - +
403D ARG* 1.3 66.2 + - - +
405D GLN* 3.4 4.5 + - - +
406D VAL* 3.2 28.7 + - - +
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Residues in contact with ARG 403 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281D VAL* 3.7 22.9 + - - -
282D PHE* 3.7 11.7 - - + -
283D THR* 5.3 4.9 - - - +
286D GLU* 2.8 36.5 + - - +
397D LEU* 3.4 37.1 + - + -
398D ASP 2.8 29.1 + - - -
399D ASN 3.1 14.5 + - - +
400D TYR* 2.7 23.9 + - + +
402D ASP* 1.3 76.7 - - - +
404D ILE* 1.3 58.9 + - - +
405D GLN 3.1 1.8 - - - -
406D VAL* 3.1 4.0 + - - +
407D LEU* 3.0 32.8 + - + +
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Residues in contact with ILE 404 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360D MET* 3.9 37.0 - - + +
363D ASP* 4.1 15.5 - - + +
364D ILE* 4.2 13.2 - - + -
400D TYR* 2.7 60.5 + - + +
401D SER* 3.5 18.2 - - - +
403D ARG* 1.3 73.7 - - - +
405D GLN* 1.3 60.2 + - - +
407D LEU* 4.4 8.1 - - + -
408D GLN* 2.9 36.8 + - - +
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Residues in contact with GLN 405 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376D LEU* 5.2 1.6 - - + -
379D ASP* 3.7 45.2 + - + +
380D LEU* 5.0 0.8 - - + -
383D MET* 3.1 26.4 - - + +
401D SER* 3.2 21.3 + - - +
402D ASP* 3.4 6.9 + - - +
403D ARG 3.1 0.4 - - - -
404D ILE* 1.3 83.1 - - + +
406D VAL* 1.3 58.9 + - - +
408D GLN* 3.4 16.7 + - - +
409D ASN* 2.9 45.7 + - - +
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Residues in contact with VAL 406 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278D LEU* 4.6 6.3 - - + -
282D PHE* 3.8 22.4 - - + -
380D LEU* 5.4 2.2 - - + -
383D MET* 3.7 21.3 - - - -
395D LEU* 5.7 0.4 - - + -
397D LEU* 3.6 20.0 - - + -
402D ASP 3.2 15.2 + - - +
403D ARG 3.1 7.3 + - - +
405D GLN* 1.3 75.6 - - - +
407D LEU* 1.3 60.5 + - - +
409D ASN* 3.4 5.0 + - - +
410D MET* 2.8 28.4 + - + +
481D TRP* 3.8 25.0 - - + -
484D LEU* 4.3 14.8 - - + -
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Residues in contact with LEU 407 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273D LEU* 4.1 12.8 - - + -
282D PHE* 3.6 31.9 - - + -
286D GLU* 4.0 35.2 - - + +
290D ALA* 4.1 18.2 - - + -
360D MET* 4.9 4.5 - - - -
364D ILE* 4.0 23.8 - - + -
403D ARG* 3.0 20.3 + - + +
404D ILE* 3.9 15.3 - - + +
406D VAL* 1.3 73.8 - - - +
408D GLN* 1.3 66.1 + - - +
410D MET* 3.4 8.7 - - - +
411D VAL* 3.0 29.3 + - - +
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Residues in contact with GLN 408 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363D ASP* 3.1 37.4 - - - +
364D ILE* 4.0 15.9 - - + +
367D ALA* 3.7 20.5 - - + +
368D THR* 6.1 0.5 - - - +
376D LEU* 4.1 16.5 - - + +
404D ILE* 2.9 32.0 + - + +
405D GLN* 3.5 19.7 + - - +
406D VAL 3.2 0.2 - - - -
407D LEU* 1.3 78.5 - - - +
409D ASN* 1.3 63.7 + - - +
411D VAL* 3.3 2.4 + - - +
412D HIS* 2.9 23.1 + - - +
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Residues in contact with ASN 409 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376D LEU* 3.2 46.2 + - - +
377D LEU 4.3 0.2 + - - -
380D LEU* 3.7 43.7 - - + +
405D GLN* 2.9 31.8 + - - +
406D VAL 3.9 3.1 - - - +
408D GLN* 1.3 79.9 - - - +
410D MET* 1.3 56.8 + - - +
412D HIS* 3.4 7.3 - - - +
413D CYS* 2.8 34.5 + - - -
477D LEU* 4.3 10.8 - - + +
481D TRP* 4.4 5.2 - - + -
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Residues in contact with MET 410 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269D THR* 4.2 11.7 - - + +
272D LEU* 3.7 30.1 - - + +
273D LEU* 3.5 44.2 - - + -
278D LEU* 3.4 32.8 - - + -
282D PHE* 4.3 7.2 - - + -
290D ALA* 5.3 0.7 - - - -
406D VAL* 2.8 20.3 + - + +
407D LEU* 3.4 13.2 - - + +
408D GLN 3.1 0.2 - - - -
409D ASN* 1.3 75.9 - - - +
411D VAL* 1.3 58.6 + - - +
413D CYS* 2.9 7.4 + - - +
414D ALA* 2.8 27.0 + - - +
481D TRP* 3.8 19.0 - - + -
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Residues in contact with VAL 411 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265D VAL* 4.4 9.4 - - + -
269D THR* 4.0 11.0 - - + +
290D ALA* 4.0 15.5 - - + +
293D ALA 5.3 0.2 - - - -
294D SER* 3.8 31.6 - - - +
297D HIS* 5.3 3.1 - - + -
364D ILE* 3.6 30.1 - - + -
368D THR* 4.3 16.8 - - + -
407D LEU 3.0 14.0 + - - +
408D GLN 4.0 1.1 - - - +
410D MET* 1.3 75.3 - - + +
412D HIS* 1.3 57.5 + - - +
414D ALA* 3.3 7.3 + - - +
415D ASP* 2.8 27.4 + - + +
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Residues in contact with HIS 412 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367D ALA 3.9 16.1 + - - +
368D THR* 4.5 14.0 + - - +
369D ASP 5.3 0.2 - - - -
370D MET* 3.8 16.8 - - - -
373D HIS* 2.8 36.8 + - + +
376D LEU* 4.0 19.1 - - + -
377D LEU 6.2 0.2 - - - -
408D GLN 2.9 17.7 + - - +
409D ASN* 3.4 9.2 - - - +
410D MET 3.1 0.2 - - - -
411D VAL* 1.3 78.0 - - - +
413D CYS* 1.3 55.4 + - - +
415D ASP* 3.3 8.5 + - - +
416D LEU* 3.0 51.3 + - + +
477D LEU* 3.5 28.7 - - + -
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Residues in contact with CYS 413 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272D LEU* 4.2 5.6 - - + -
409D ASN* 2.8 20.5 + - - -
410D MET* 3.3 9.0 - - - +
412D HIS* 1.3 72.1 - - - +
414D ALA* 1.3 66.5 + - - +
416D LEU 3.1 4.5 + - - -
417D SER 3.0 18.5 + - - -
477D LEU* 3.7 33.7 - - - -
478D TRP* 3.3 34.0 - - + -
481D TRP* 3.8 33.4 - - - -
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Residues in contact with ALA 414 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264D ASP* 5.4 0.7 - - - +
265D VAL* 3.8 24.8 - - + +
268D SER* 3.9 14.3 - - - -
269D THR* 3.4 29.4 - - - +
272D LEU* 4.2 4.9 - - + +
410D MET 2.8 11.1 + - - +
411D VAL 3.5 7.6 - - - +
413D CYS* 1.3 77.2 - - - +
415D ASP* 1.3 59.5 + - - +
417D SER* 2.8 27.3 + - - -
418D ASN* 5.5 0.9 + - - -
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Residues in contact with ASP 415 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256D TYR* 4.3 7.3 + - - -
261D HIS* 2.9 17.8 + - - -
265D VAL* 3.9 9.8 - - + +
297D HIS* 2.8 17.3 + - + +
368D THR* 4.1 21.7 - - + +
411D VAL 2.8 17.7 + - - +
412D HIS* 3.6 11.1 + - - +
413D CYS 3.2 0.2 - - - -
414D ALA* 1.3 76.9 - - - +
416D LEU* 1.3 69.2 + - + +
417D SER 3.4 1.7 + - - -
418D ASN* 5.2 2.4 + - - +
2007D ZN 2.2 36.0 - - - -
2008D MG 4.3 1.7 - - - -
3004D ZAR 5.9 1.4 - - - -
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Residues in contact with LEU 416 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370D MET* 4.1 14.1 - - + -
412D HIS* 3.0 46.3 + - + +
413D CYS 3.1 4.9 - - - +
415D ASP* 1.3 87.5 - - + +
417D SER* 1.3 57.5 + - - +
418D ASN* 3.6 3.1 - - - +
419D PRO* 4.0 4.5 - - - +
469D PHE* 3.7 25.6 - - + -
473D ILE* 3.9 21.3 - - + -
474D VAL* 3.7 19.9 - - + +
477D LEU* 3.8 17.3 - - + -
478D TRP* 3.2 14.2 + - - -
3004D ZAR 4.8 14.1 - - + -
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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
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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) + - + + + + + -
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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