Contacts of the helix formed by residues 372 - 385 (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 LYS 372 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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324G SER* 3.7 23.1 + - - -
366G LEU* 3.4 28.3 - - - +
367G ALA* 4.7 8.7 - - - +
369G ASP* 3.0 14.4 + - + +
371G SER* 1.3 88.3 + - - +
373G HIS* 1.3 64.9 + - - +
374G MET 3.4 2.2 - - - -
375G ASN* 3.4 15.9 + - + +
376G LEU* 3.0 28.5 + - + +
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Residues in contact with HIS 373 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369G ASP 3.9 1.2 + - - -
370G MET* 3.0 31.7 + - + +
371G SER 3.4 0.4 - - - -
372G LYS* 1.3 77.2 - - - +
374G MET* 1.3 77.1 + - + +
376G LEU* 3.2 4.7 + - - +
377G LEU* 2.8 50.0 + - + +
412G HIS* 2.9 36.1 + + + +
472G TYR 4.5 2.2 + - - -
473G ILE* 3.7 44.2 + - + +
477G LEU* 3.9 25.1 - - + -
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Residues in contact with MET 374 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386D THR* 6.2 1.6 - - - -
387D LYS 4.1 23.3 - - - +
388D LYS* 5.4 7.4 - - + -
389D VAL* 5.1 15.0 - - + +
371G SER 5.1 2.8 + - - +
372G LYS 3.4 0.6 - - - -
373G HIS* 1.3 98.8 - - + +
375G ASN* 1.3 61.6 + - - +
377G LEU* 3.4 11.0 + - - +
378G ALA* 2.9 29.7 + - - +
472G TYR* 4.6 7.6 - - + +
473G ILE* 4.6 14.1 - - + -
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Residues in contact with ASN 375 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371G SER 4.5 4.9 + - - -
372G LYS* 3.4 20.7 + - + +
373G HIS 3.3 0.4 - - - -
374G MET* 1.3 75.9 - - - +
376G LEU* 1.3 68.5 + - - +
378G ALA* 3.1 8.3 + - - +
379G ASP* 2.9 32.4 + - - +
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Residues in contact with LEU 376 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367G ALA* 3.6 37.2 - - + +
372G LYS* 3.0 20.3 + - + +
373G HIS* 3.5 4.5 - - - +
375G ASN* 1.3 76.7 - - - +
377G LEU* 1.3 58.5 + - - +
379G ASP* 3.3 9.0 + - - +
380G LEU* 3.0 22.9 + - - +
405G GLN* 5.2 3.6 - - + -
408G GLN* 4.1 24.7 - - + +
409G ASN* 3.2 42.9 + - - +
412G HIS* 4.0 28.5 - - + +
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Residues in contact with LEU 377 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373G HIS* 2.8 42.2 + - + +
374G MET* 3.7 12.6 - - - +
376G LEU* 1.3 73.3 - - - +
378G ALA* 1.3 60.7 + - - +
380G LEU* 3.1 7.2 + - + +
381G LYS* 2.9 47.5 + - - +
409G ASN* 4.3 2.7 + - - -
476G PRO* 3.7 28.3 - - + +
477G LEU* 3.8 18.4 - - + +
480G THR* 3.4 31.0 - - + +
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Residues in contact with ALA 378 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374G MET 2.9 15.6 + - - +
375G ASN* 3.3 12.1 - - - +
377G LEU* 1.3 76.7 - - - +
379G ASP* 1.3 64.3 + - - +
381G LYS* 3.2 12.4 + - - +
382G THR* 3.1 25.9 + - - -
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Residues in contact with ASP 379 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375G ASN* 2.9 23.3 + - - +
376G LEU* 3.7 9.3 - - + +
378G ALA* 1.3 77.5 - - - +
380G LEU* 1.3 62.0 + - - +
382G THR* 3.4 8.9 + - - -
383G MET* 3.0 22.7 + - - +
405G GLN* 3.7 35.6 + - + +
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Residues in contact with LEU 380 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376G LEU 3.0 13.9 + - - +
377G LEU* 3.1 10.3 + - + +
379G ASP* 1.3 78.3 - - - +
381G LYS* 1.3 57.5 + - - +
383G MET* 3.1 13.8 + - - +
384G VAL* 2.9 32.1 + - + +
405G GLN* 5.1 2.5 - - + +
406G VAL* 5.4 2.7 - - - -
409G ASN* 3.7 39.7 - - + +
477G LEU* 4.4 12.8 - - + -
480G THR* 3.5 28.9 - - + -
481G TRP* 4.1 17.5 - - + +
484G LEU* 4.2 26.5 - - + -
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Residues in contact with LYS 381 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385D GLU* 5.5 11.2 - - + +
377G LEU* 2.9 39.2 + - + +
378G ALA* 3.2 11.2 + - - +
380G LEU* 1.3 76.4 - - - +
382G THR* 1.3 60.8 + - - +
384G VAL* 3.0 15.5 + - - +
385G GLU* 3.2 20.4 + - + +
476G PRO* 5.0 5.0 - - - +
480G THR* 3.8 30.7 - - + +
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Residues in contact with THR 382 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378G ALA 3.1 15.0 + - - -
379G ASP* 3.6 13.5 + - - -
381G LYS* 1.3 76.4 - - - +
383G MET* 1.3 57.6 + - - +
385G GLU* 3.0 30.9 + - - +
386G THR* 3.4 14.0 + - + +
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Residues in contact with MET 383 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379G ASP 3.0 12.7 + - - +
380G LEU* 3.4 16.2 - - + +
381G LYS 3.0 0.6 - - - -
382G THR* 1.3 75.8 - - - +
384G VAL* 1.3 55.4 + - - +
385G GLU 2.6 18.7 - - - +
386G THR* 4.0 5.4 + - - +
387G LYS* 3.7 14.4 - - - +
397G LEU* 4.4 8.1 - - + -
402G ASP* 3.2 48.2 - - + +
405G GLN* 3.1 26.9 - - - +
406G VAL* 3.7 25.8 - - - -
484G LEU* 4.3 14.8 - - + +
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Residues in contact with VAL 384 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380G LEU* 2.9 20.8 + - + +
381G LYS* 3.0 7.8 + - - +
383G MET* 1.3 72.3 - - - +
385G GLU* 1.3 63.4 + - + +
387G LYS* 3.0 29.2 + - - +
480G THR* 3.7 33.0 - - + +
483G ASP* 3.5 35.0 - - + +
484G LEU* 4.1 22.9 - - + +
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Residues in contact with GLU 385 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381G LYS* 3.2 14.3 + - - +
382G THR* 3.0 19.7 + - - +
383G MET 2.6 16.6 - - - +
384G VAL* 1.3 73.1 - - + +
386G THR* 1.3 79.0 + - + +
387G LYS 2.9 5.6 - - - -
381K LYS* 6.1 3.4 - - - +
385K GLU* 5.6 1.4 - - - +
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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