Contacts of the helix formed by residues 399 - 416 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398A ASP* 1.3 99.0 - - - +
400A TYR* 1.3 63.3 - - - +
401A SER* 2.6 46.7 + - - +
402A ASP* 3.2 23.9 + - - +
403A ARG* 3.1 27.9 + - - +
399E ASN* 6.5 0.7 - - + -
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Residues in contact with TYR 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A GLU* 5.1 7.6 - - - -
359A LYS* 3.8 29.6 - - + +
360A MET* 3.7 31.8 - - + +
363A ASP* 2.9 24.6 + - - -
399A ASN* 1.3 70.0 - - - +
401A SER* 1.3 60.2 + - - +
402A ASP 2.9 4.3 - - - -
403A ARG* 2.7 24.9 + - + +
404A ILE* 2.7 65.6 + - + +
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Residues in contact with SER 401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399A ASN* 2.6 22.1 + - - +
400A TYR* 1.3 83.3 - - - +
402A ASP* 1.3 60.2 + - - +
404A ILE* 3.6 14.0 - - - +
405A GLN* 3.2 30.4 + - - +
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Residues in contact with ASP 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A MET* 3.2 27.1 - - + +
388A LYS* 5.1 3.3 + - - -
397A LEU* 4.1 17.9 - - + +
398A ASP* 3.4 17.2 - - - +
399A ASN* 3.2 28.0 + - - +
400A TYR 2.9 0.8 - - - -
401A SER* 1.3 83.1 + - - +
403A ARG* 1.3 67.0 + - - +
405A GLN* 3.4 5.0 + - - +
406A VAL* 3.2 26.9 + - - +
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Residues in contact with ARG 403 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281A VAL* 3.7 23.0 + - - -
282A PHE* 3.7 12.8 - - + -
283A THR* 5.3 4.5 - - - +
286A GLU* 2.8 37.5 + - - +
397A LEU* 3.4 38.1 + - + -
398A ASP 2.8 28.3 + - - -
399A ASN 3.1 14.1 + - - +
400A TYR* 2.7 24.1 + - + +
402A ASP* 1.3 76.0 - - - +
404A ILE* 1.3 59.2 + - - +
405A GLN 3.1 1.6 - - - -
406A VAL* 3.1 3.8 + - - +
407A LEU* 2.9 32.5 + - + +
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Residues in contact with ILE 404 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360A MET* 3.9 37.2 - - + +
363A ASP* 4.1 14.6 - - + +
364A ILE* 4.2 13.2 - - + -
400A TYR* 2.7 58.8 + - + +
401A SER* 3.6 17.7 - - - +
403A ARG* 1.3 72.8 - - - +
405A GLN* 1.3 61.0 + - - +
407A LEU* 4.3 8.3 - - + -
408A GLN* 2.9 36.1 + - - +
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Residues in contact with GLN 405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376A LEU* 5.2 1.3 - - + -
379A ASP* 3.7 45.6 + - + +
380A LEU* 5.1 1.1 - - + -
383A MET* 3.1 27.6 - - + +
401A SER* 3.2 21.3 + - - +
402A ASP* 3.4 7.1 + - - +
403A ARG 3.1 0.2 - - - -
404A ILE* 1.3 83.1 - - + +
406A VAL* 1.3 61.5 + - - +
408A GLN* 3.4 16.0 + - - +
409A ASN* 2.9 42.2 + - - +
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Residues in contact with VAL 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278A LEU* 4.6 7.6 - - + -
282A PHE* 3.8 22.7 - - + -
380A LEU* 5.4 2.2 - - + -
383A MET* 3.7 21.3 - - - -
395A LEU* 5.7 0.2 - - + -
397A LEU* 3.6 19.3 - - + -
402A ASP 3.2 15.5 + - - +
403A ARG 3.1 7.1 + - - +
405A GLN* 1.3 75.3 - - - +
407A LEU* 1.3 54.4 + - - +
409A ASN* 3.4 5.0 + - - +
410A MET* 2.8 36.6 + - + +
481A TRP* 3.8 24.3 - - + -
484A LEU* 4.4 14.1 - - + -
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Residues in contact with LEU 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273A LEU* 4.1 12.6 - - + -
282A PHE* 3.6 32.3 - - + -
286A GLU* 4.0 35.4 - - + +
289A ALA* 5.8 0.2 - - + -
290A ALA* 4.1 18.2 - - + -
360A MET* 5.1 4.5 - - - -
364A ILE* 4.0 23.3 - - + -
403A ARG* 2.9 19.9 + - + +
404A ILE* 3.8 15.3 - - + +
406A VAL* 1.3 72.7 - - - +
408A GLN* 1.3 66.3 + - - +
410A MET* 3.5 7.9 - - - +
411A VAL* 3.0 29.8 + - - +
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Residues in contact with GLN 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363A ASP* 3.1 38.0 - - - +
364A ILE* 4.0 15.1 - - + +
367A ALA* 3.6 20.1 - - + +
368A THR* 6.1 0.3 - - - +
376A LEU* 4.1 16.6 - - + +
404A ILE* 2.9 31.2 + - + +
405A GLN* 3.5 19.3 - - - +
407A LEU* 1.3 78.6 - - - +
409A ASN* 1.3 63.4 + - - +
411A VAL* 3.3 2.3 + - - +
412A HIS* 2.9 23.8 + - - +
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Residues in contact with ASN 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376A LEU* 3.2 47.1 + - - +
377A LEU 4.3 0.7 + - - -
380A LEU* 3.7 43.2 - - + +
405A GLN* 2.9 32.0 + - - +
406A VAL 3.9 3.1 - - - +
408A GLN* 1.3 80.0 - - - +
410A MET* 1.3 57.1 + - - +
412A HIS* 3.3 7.8 + - - +
413A CYS* 2.8 34.4 + - - -
477A LEU* 4.3 9.4 - - + +
481A TRP* 4.4 5.4 - - + -
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Residues in contact with MET 410 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269A THR* 4.2 12.3 - - + +
272A LEU* 3.7 28.0 - - + +
273A LEU* 3.6 42.2 - - + -
278A LEU* 3.5 32.3 - - + -
282A PHE* 4.3 7.6 - - + -
290A ALA* 5.3 1.1 - - - -
406A VAL* 2.8 20.5 + - + +
407A LEU* 3.5 14.4 - - + +
408A GLN 3.1 0.2 - - - -
409A ASN* 1.3 76.7 - - - +
411A VAL* 1.3 58.4 + - - +
413A CYS* 3.0 7.6 + - - +
414A ALA* 2.9 26.5 + - - +
481A TRP* 3.8 18.6 - - + -
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Residues in contact with VAL 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265A VAL* 4.4 9.2 - - + -
269A THR* 4.0 10.5 - - + +
290A ALA* 4.0 15.7 - - + +
293A ALA 5.3 0.2 - - - -
294A SER* 3.7 31.6 - - - +
297A HIS* 5.2 2.9 - - + -
364A ILE* 3.5 29.8 - - + -
368A THR* 4.3 16.8 - - + -
407A LEU 3.0 15.5 + - - +
408A GLN 4.0 1.3 - - - +
410A MET* 1.3 75.4 - - + +
412A HIS* 1.3 56.2 + - - +
414A ALA* 3.5 6.6 - - - +
415A ASP* 2.8 28.2 + - + +
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Residues in contact with HIS 412 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367A ALA 3.9 17.4 + - - +
368A THR* 4.5 14.0 + - + +
369A ASP 5.2 0.2 - - - -
370A MET* 3.9 17.0 - - - -
373A HIS* 2.8 37.9 + - + +
376A LEU* 4.0 19.7 - - + -
408A GLN 2.9 18.0 + - - +
409A ASN* 3.4 8.7 - - - +
411A VAL* 1.3 76.5 - - - +
413A CYS* 1.3 57.4 + - - +
415A ASP* 3.3 9.0 + - - +
416A LEU* 3.0 47.9 + - + +
477A LEU* 3.4 29.2 - - + -
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Residues in contact with CYS 413 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272A LEU* 4.2 4.7 - - + -
409A ASN* 2.8 20.7 + - - +
410A MET* 3.3 8.5 - - - +
412A HIS* 1.3 73.7 - - - +
414A ALA* 1.3 64.5 + - - +
416A LEU 3.1 4.3 + - - -
417A SER 3.0 18.7 + - - -
477A LEU* 3.7 33.0 - - - -
478A TRP* 3.3 32.2 - - + -
481A TRP* 3.9 34.5 - - + -
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Residues in contact with ALA 414 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264A ASP* 5.4 0.9 - - - +
265A VAL* 3.7 25.0 - - + +
268A SER* 3.9 13.2 - - - -
269A THR* 3.4 29.6 - - - +
272A LEU* 4.2 5.3 - - + +
410A MET 2.9 11.0 + - - +
411A VAL 3.5 6.5 - - - +
413A CYS* 1.3 75.9 - - - +
415A ASP* 1.3 62.3 + - - +
417A SER* 2.8 27.5 + - - -
418A ASN* 5.5 0.7 + - - -
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Residues in contact with ASP 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256A TYR* 4.3 6.9 + - - -
261A HIS* 2.9 18.4 + - - -
265A VAL* 3.9 9.8 - - + +
297A HIS* 2.7 17.6 + - + -
368A THR* 4.0 21.0 - - + +
411A VAL 2.8 18.1 + - - +
412A HIS* 3.6 11.2 + - - +
414A ALA* 1.3 77.3 - - - +
416A LEU* 1.3 66.3 + - + +
417A SER 3.4 2.0 + - - -
418A ASN* 5.2 2.3 + - - +
2001A ZN 2.2 35.7 - - - -
3001A ZAR 6.0 1.4 - - - -
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Residues in contact with LEU 416 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370A MET* 4.0 14.8 - - - -
412A HIS* 3.0 47.4 + - + +
413A CYS 3.1 5.3 + - - +
415A ASP* 1.3 88.0 - - + +
417A SER* 1.3 58.2 + - - +
418A ASN* 3.6 2.5 - - - -
419A PRO* 4.0 4.4 - - - +
469A PHE* 3.6 26.9 - - + -
473A ILE* 3.9 21.1 - - + -
474A VAL* 3.7 19.7 - - + +
477A LEU* 3.8 17.3 - - + -
478A TRP* 3.2 14.0 + - - -
3001A ZAR 4.8 13.5 - - + -
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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