Contacts of the helix formed by residues 372 - 385 (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 LYS 372 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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324D SER* 3.7 23.3 + - - -
366D LEU* 3.5 27.6 - - - +
367D ALA* 4.7 9.9 - - - +
369D ASP* 2.9 13.4 + - + +
371D SER* 1.3 87.1 + - - +
373D HIS* 1.3 64.1 + - - +
374D MET 3.4 2.0 - - - -
375D ASN* 3.4 15.8 + - + +
376D LEU* 3.0 28.3 + - + +
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Residues in contact with HIS 373 (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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369D ASP 3.9 1.2 + - - -
370D MET* 3.1 31.5 + - + +
371D SER 3.4 0.4 - - - -
372D LYS* 1.3 77.9 - - - +
374D MET* 1.3 81.3 + - + +
376D LEU* 3.2 4.4 + - - +
377D LEU* 2.9 41.9 + - + +
412D HIS* 2.8 35.7 + + + +
472D TYR 4.6 2.4 + - - -
473D ILE* 3.6 44.4 + - + +
477D LEU* 3.9 25.4 - - + -
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Residues in contact with MET 374 (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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371D SER 5.1 2.8 + - - +
372D LYS 3.4 0.4 - - - -
373D HIS* 1.3 97.6 - - + +
375D ASN* 1.3 61.4 + - - +
377D LEU* 3.4 11.7 + - - +
378D ALA* 2.9 28.6 + - - +
472D TYR* 4.7 7.4 - - + +
473D ILE* 4.5 14.1 - - + -
386K THR* 6.6 0.4 - - - -
387K LYS 4.7 16.2 - - - +
388K LYS* 5.7 6.7 - - + -
389K VAL 5.7 7.0 - - - +
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Residues in contact with ASN 375 (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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371D SER 4.5 4.9 + - - -
372D LYS* 3.4 20.6 + - + +
373D HIS 3.3 0.6 - - - -
374D MET* 1.3 76.6 - - - +
376D LEU* 1.3 66.5 + - - +
378D ALA* 3.1 8.0 + - - +
379D ASP* 2.9 33.7 + - - +
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Residues in contact with LEU 376 (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* 3.6 36.8 - - + +
372D LYS* 3.0 21.1 + - + +
373D HIS* 3.6 4.5 - - - +
375D ASN* 1.3 77.4 - - - +
377D LEU* 1.3 58.8 + - - +
379D ASP* 3.4 6.8 + - - +
380D LEU 3.0 21.8 + - - -
405D GLN* 5.2 3.4 - - + -
408D GLN* 4.1 25.6 - - + +
409D ASN* 3.2 43.7 + - - +
412D HIS* 4.0 28.5 - - + +
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Residues in contact with LEU 377 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373D HIS* 2.9 42.4 + - + +
374D MET* 3.7 11.2 - - - +
376D LEU* 1.3 73.3 - - - +
378D ALA* 1.3 67.7 + - - +
380D LEU* 3.2 7.1 + - + +
381D LYS* 2.9 42.2 + - - +
409D ASN* 4.3 2.7 + - - -
412D HIS* 6.2 0.2 - - - -
472D TYR 5.9 0.2 - - - +
476D PRO* 3.8 27.4 - - + +
477D LEU* 3.8 17.9 - - + +
480D THR* 3.4 31.4 - - + +
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Residues in contact with ALA 378 (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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374D MET 2.9 18.8 + - - +
375D ASN* 3.1 10.1 + - - +
377D LEU* 1.3 77.3 - - - +
379D ASP* 1.3 64.0 + - - +
381D LYS* 3.2 11.5 + - - +
382D THR* 3.0 26.2 + - - -
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Residues in contact with ASP 379 (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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375D ASN* 2.9 25.3 + - - +
376D LEU* 3.8 8.2 - - + +
378D ALA* 1.3 78.4 - - - +
380D LEU* 1.3 62.9 + - - +
382D THR* 3.4 9.7 + - - -
383D MET* 3.0 23.0 + - - +
405D GLN* 3.7 35.2 + - + +
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Residues in contact with LEU 380 (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 3.0 13.9 + - - +
377D LEU* 3.2 10.3 + - + +
379D ASP* 1.3 78.3 - - - +
381D LYS* 1.3 57.1 + - - +
383D MET* 3.1 14.1 + - - +
384D VAL* 2.9 32.6 + - + +
405D GLN* 5.0 2.2 - - - +
406D VAL* 5.4 2.5 - - - -
409D ASN* 3.7 38.3 - - + +
477D LEU* 4.5 13.0 - - + +
480D THR* 3.4 27.6 - - + +
481D TRP* 4.1 18.6 - - + +
484D LEU* 4.2 25.8 - - + -
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Residues in contact with LYS 381 (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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377D LEU* 2.9 37.2 + - + +
378D ALA* 3.2 10.5 + - - +
380D LEU* 1.3 74.5 - - - +
382D THR* 1.3 65.6 + - - +
384D VAL* 3.0 15.6 + - - +
385D GLU* 3.2 19.8 + - - +
476D PRO* 5.1 5.0 - - - +
480D THR* 3.8 30.5 - - + +
385K GLU* 5.7 10.1 - - - +
386K THR 5.9 1.2 - - - +
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Residues in contact with THR 382 (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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378D ALA 3.0 14.8 + - - -
379D ASP* 3.6 13.3 + - - -
381D LYS* 1.3 77.3 - - - +
383D MET* 1.3 56.0 + - - +
385D GLU* 3.0 31.0 + - - +
386D THR* 3.4 14.0 + - + +
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Residues in contact with MET 383 (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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379D ASP 3.0 12.5 + - - +
380D LEU* 3.4 16.8 - - - +
381D LYS 3.0 0.6 - - - -
382D THR* 1.3 75.3 - - - +
384D VAL* 1.3 54.9 + - - +
385D GLU 2.6 18.6 - - - +
386D THR* 4.0 4.8 + - - +
387D LYS* 3.7 14.7 - - - +
397D LEU* 4.4 8.3 - - + -
402D ASP* 3.2 49.4 - - + +
405D GLN* 3.1 25.8 - - - +
406D VAL* 3.7 25.8 - - - -
484D LEU* 4.3 14.5 - - + +
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Residues in contact with VAL 384 (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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380D LEU* 2.9 22.1 + - + +
381D LYS* 3.0 7.5 + - - +
383D MET* 1.3 72.9 - - - +
385D GLU* 1.3 62.5 + - + +
387D LYS* 3.0 29.6 + - - +
480D THR* 3.7 32.5 - - + +
483D ASP* 3.5 33.9 - - + +
484D LEU* 4.1 21.3 - - + +
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Residues in contact with GLU 385 (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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381D LYS* 3.2 14.8 + - - +
382D THR* 3.0 20.1 + - - +
383D MET 2.6 16.8 - - - +
384D VAL* 1.3 73.3 - - + +
386D THR* 1.3 79.5 + - + +
387D LYS 2.9 6.1 - - - -
381G LYS* 5.5 10.5 - - + +
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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
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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