Contacts of the helix formed by residues 350 - 367 (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 THR 350 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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348G ASN 4.1 1.5 + - - +
349G LEU* 1.3 75.9 - - - +
351G LYS* 1.3 64.6 + - - +
352G LYS* 3.3 25.5 - - - +
353G GLN* 2.9 43.7 + - - +
354G ARG* 2.9 19.8 + - - +
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Residues in contact with LYS 351 (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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311F ASN 5.8 4.9 + - - -
449F MET* 6.2 2.2 - - - +
349G LEU 3.7 1.0 + - - -
350G THR* 1.3 73.2 - - - +
352G LYS* 1.3 74.6 + - + +
354G ARG* 3.3 15.4 + - - +
355G GLN* 3.1 49.0 + - + +
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Residues in contact with LYS 352 (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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350G THR* 3.1 23.3 - - - +
351G LYS* 1.3 97.0 - - + +
353G GLN* 1.3 57.6 + - + +
355G GLN* 3.2 17.0 + - - +
356G SER* 3.0 30.6 + - - -
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Residues in contact with GLN 353 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232G PHE* 4.3 20.7 - - - -
285G LEU* 3.8 25.6 - - + +
348G ASN 4.7 0.9 - - - +
349G LEU* 3.4 22.9 - - + +
350G THR* 2.9 53.3 + - - +
352G LYS* 1.3 73.7 - - + +
354G ARG* 1.3 61.3 + - - +
356G SER* 3.2 2.0 + - - -
357G LEU* 2.9 32.5 + - - +
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Residues in contact with ARG 354 (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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344G ASP* 3.6 18.0 + - - -
346G PHE* 2.7 46.4 + - + +
347G GLN* 3.5 10.3 + - - +
349G LEU* 3.5 29.2 - - + +
350G THR 2.9 15.2 + - - +
351G LYS* 3.6 14.6 - - - +
353G GLN* 1.3 76.6 - - - +
355G GLN* 1.3 59.3 + - + +
357G LEU* 3.9 7.2 - - - +
358G ARG* 3.0 28.8 + - - +
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Residues in contact with GLN 355 (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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311F ASN* 5.5 3.8 - - - +
351G LYS* 3.1 44.6 + - + +
352G LYS* 3.4 15.2 + - - +
353G GLN 3.1 0.2 - - - -
354G ARG* 1.3 76.1 - - + +
356G SER* 1.3 65.4 + - - +
358G ARG* 3.4 6.7 + - - +
359G LYS* 3.0 22.9 + - - +
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Residues in contact with SER 356 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285G LEU* 3.9 16.7 - - - +
352G LYS 3.0 13.8 + - - -
353G GLN* 3.2 6.7 + - - -
355G GLN* 1.3 72.7 - - - +
357G LEU* 1.3 67.8 + - - +
359G LYS* 3.1 6.7 + - - +
360G MET* 2.9 37.3 + - - +
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Residues in contact with LEU 357 (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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285G LEU* 3.8 14.8 - - + +
288G LEU* 3.5 36.8 - - + -
289G ALA* 3.8 17.0 - - + +
292G PHE* 4.6 1.6 - - + -
335G PHE* 5.3 3.4 - - + -
346G PHE* 3.4 41.7 - - + -
349G LEU* 4.7 1.8 - - + -
353G GLN 2.9 17.7 + - - +
354G ARG* 3.9 6.1 - - - +
356G SER* 1.3 78.0 - - - +
358G ARG* 1.3 64.6 + - - +
360G MET* 3.3 9.9 + - - +
361G VAL* 2.9 42.6 + - + +
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Residues in contact with ARG 358 (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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313F ASN* 6.0 1.1 - - - -
317F ALA* 3.1 27.3 + - - +
318F LEU* 3.4 19.1 + - - +
321F ASN* 3.7 10.9 - - - +
322F ASP* 3.1 27.3 + - - +
335G PHE* 3.2 61.0 - - + +
354G ARG 3.0 19.2 + - - +
355G GLN* 3.7 5.8 - - - +
357G LEU* 1.3 77.6 - - - +
359G LYS* 1.3 61.9 + - - +
361G VAL* 3.8 0.5 - - - +
362G ILE* 3.0 41.8 + - + +
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Residues in contact with LYS 359 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322F ASP* 5.9 1.8 - - - +
355G GLN 3.0 14.0 + - - +
356G SER* 3.5 9.6 - - - +
358G ARG* 1.3 78.3 - - - +
360G MET* 1.3 58.4 + - + +
362G ILE* 3.3 6.7 + - + +
363G ASP* 2.9 51.7 + - - +
400G TYR* 3.7 30.7 - - + +
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Residues in contact with MET 360 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285G LEU* 3.9 24.7 - - + +
286G GLU* 3.9 30.1 - - + +
289G ALA* 3.9 17.7 - - + -
356G SER* 2.9 40.4 + - - +
357G LEU* 3.9 10.3 - - - +
359G LYS* 1.3 72.2 - - + +
361G VAL* 1.3 57.5 + - - +
363G ASP* 3.2 2.1 + - - +
364G ILE* 2.8 38.7 + - + +
400G TYR* 3.8 30.7 - - + +
404G ILE* 3.9 18.4 - - + -
407G LEU* 5.0 3.8 - - - -
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Residues in contact with VAL 361 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289G ALA* 3.7 28.9 - - - +
292G PHE* 3.8 20.6 - - + -
293G ALA* 4.2 14.6 - - + -
296G ILE* 4.1 14.8 - - + -
331G LEU* 3.8 11.9 - - + -
335G PHE* 3.6 25.1 - - + -
357G LEU* 2.9 29.4 + - + +
360G MET* 1.3 73.9 - - - +
362G ILE* 1.3 56.9 + - - +
364G ILE* 3.2 1.3 + - - +
365G VAL* 2.9 30.7 + - - +
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Residues in contact with ILE 362 (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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321F ASN* 3.5 51.8 - - + +
322F ASP* 3.9 6.7 - - + +
323F SER* 4.6 2.0 - - - +
331G LEU* 3.7 9.6 - - + -
335G PHE* 3.7 15.9 - - + -
358G ARG* 3.0 46.8 + - + +
359G LYS* 3.7 6.1 - - + +
361G VAL* 1.3 75.0 - - - +
363G ASP* 1.3 69.7 + - - +
366G LEU* 3.0 42.9 + - + +
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Residues in contact with ASP 363 (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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359G LYS* 2.9 36.9 + - - +
360G MET 3.6 3.4 - - - +
362G ILE* 1.3 81.5 - - - +
364G ILE* 1.3 64.4 + - - +
366G LEU* 4.3 5.8 - - - +
367G ALA* 3.5 12.6 + - - +
400G TYR* 2.9 23.4 + - - -
404G ILE* 4.1 13.8 - - + +
408G GLN* 3.0 26.9 - - - +
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Residues in contact with ILE 364 (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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289G ALA 4.5 0.9 - - - -
290G ALA* 3.9 29.2 - - + +
293G ALA* 3.9 14.8 - - + -
360G MET* 2.8 26.9 + - + +
361G VAL 3.8 2.7 - - - +
363G ASP* 1.3 75.0 - - - +
365G VAL* 1.3 68.4 + - - +
367G ALA* 2.9 18.7 + - - +
368G THR* 3.5 6.9 + - - +
404G ILE* 4.2 11.4 - - + -
407G LEU* 4.0 28.5 - - + +
408G GLN* 3.9 14.4 - - + +
411G VAL* 3.5 36.3 - - + -
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Residues in contact with VAL 365 (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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293G ALA* 3.8 32.5 - - + +
296G ILE* 4.4 3.8 - - + -
297G HIS* 4.1 27.6 - - + +
327G GLU* 3.8 17.8 - - + +
330G HIS* 4.5 3.6 - - + -
331G LEU* 3.6 34.8 - - + +
361G VAL* 2.9 18.5 + - + +
364G ILE* 1.3 76.0 - - + +
366G LEU* 1.3 62.2 + - - +
368G THR* 2.6 33.4 + - - +
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Residues in contact with LEU 366 (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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321F ASN* 5.2 1.1 - - + -
323F SER* 4.5 13.2 - - - +
324G SER* 4.3 7.4 - - - +
327G GLU* 4.2 6.7 - - + -
328G ASN* 3.9 39.3 - - - +
331G LEU* 3.7 17.3 - - + -
362G ILE* 3.0 38.4 + - + +
363G ASP* 4.3 6.1 - - - +
365G VAL* 1.3 77.3 - - - +
367G ALA* 1.3 58.8 + - - +
368G THR 3.2 0.2 - - - -
369G ASP* 3.4 12.6 - - - +
372G LYS* 3.4 26.3 - - - +
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Residues in contact with ALA 367 (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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363G ASP 3.5 12.8 + - - +
364G ILE 2.9 13.2 + - - +
366G LEU* 1.3 77.6 - - - +
368G THR* 1.3 57.5 + - - +
369G ASP 3.1 12.3 + - - +
372G LYS* 4.7 8.5 - - - +
376G LEU* 3.6 28.3 - - + +
408G GLN* 3.7 30.3 - - + +
412G HIS* 3.9 8.3 + - - -
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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