Contacts of the helix formed by residues 350 - 366 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348B ASN 4.1 0.9 + - - +
349B LEU* 1.3 75.3 - - - +
351B LYS* 1.3 64.7 + - - +
352B LYS* 3.3 25.9 - - - +
353B GLN* 2.9 43.7 + - - +
354B ARG* 2.9 20.1 + - - +
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Residues in contact with LYS 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311A ASN 6.0 2.0 - - - -
349B LEU 3.7 0.8 + - - -
350B THR* 1.3 73.2 - - - +
352B LYS* 1.3 75.7 + - + +
354B ARG* 3.3 15.3 + - - +
355B GLN* 3.1 48.6 + - + +
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Residues in contact with LYS 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350B THR* 3.1 23.7 - - - +
351B LYS* 1.3 97.4 - - + +
353B GLN* 1.3 63.5 + - + +
355B GLN* 3.2 17.0 + - - +
356B SER* 3.0 26.8 + - - +
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Residues in contact with GLN 353 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B PHE* 4.3 20.9 - - - -
285B LEU* 3.7 25.4 - - + +
348B ASN 4.7 0.9 - - - +
349B LEU* 3.4 22.8 - - + +
350B THR* 2.9 52.7 + - + +
352B LYS* 1.3 73.4 - - + +
354B ARG* 1.3 62.4 + - - +
356B SER* 3.2 2.4 + - - -
357B LEU* 2.9 32.0 + - - +
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Residues in contact with ARG 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344B ASP* 3.6 17.8 + - - -
346B PHE* 2.6 45.6 + - + +
347B GLN* 3.5 9.8 + - - +
349B LEU* 3.5 29.8 - - + +
350B THR 2.9 15.2 + - - +
351B LYS* 3.6 15.3 - - - +
353B GLN* 1.3 76.8 - - - +
355B GLN* 1.3 62.6 + - + +
357B LEU* 3.9 7.2 - - - +
358B ARG* 3.0 24.9 + - - +
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Residues in contact with GLN 355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351B LYS* 3.1 45.8 + - + +
352B LYS* 3.4 14.4 - - - +
353B GLN 3.2 0.2 - - - -
354B ARG* 1.3 78.1 - - + +
356B SER* 1.3 62.2 + - - +
358B ARG* 3.3 7.7 + - - +
359B LYS* 3.0 22.1 + - - +
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Residues in contact with SER 356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B LEU* 3.8 17.8 - - - +
352B LYS* 3.0 13.4 + - - +
353B GLN* 3.7 6.5 - - - -
355B GLN* 1.3 73.3 - - - +
357B LEU* 1.3 61.9 + - - +
359B LYS* 3.1 7.0 + - - +
360B MET* 2.9 43.3 + - - +
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Residues in contact with LEU 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285B LEU* 3.9 15.2 - - + +
288B LEU* 3.5 37.0 - - + -
289B ALA* 3.8 17.0 - - + +
292B PHE* 4.7 1.3 - - + -
335B PHE* 5.3 3.6 - - + -
346B PHE* 3.4 41.7 - - + -
349B LEU* 4.7 1.8 - - + -
353B GLN 2.9 17.8 + - - +
354B ARG* 3.9 6.7 - - - +
356B SER* 1.3 75.9 - - - +
358B ARG* 1.3 60.5 + - - +
360B MET* 3.9 9.7 - - - +
361B VAL* 2.8 47.7 + - + +
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Residues in contact with ARG 358 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313A ASN* 6.0 1.6 - - - -
317A ALA 3.2 25.1 + - - -
318A LEU* 3.4 22.2 + - - +
321A ASN* 3.8 8.5 + - - +
322A ASP* 3.3 26.8 + - - +
335B PHE* 3.2 61.0 - - + +
354B ARG 3.0 18.1 + - - +
355B GLN* 3.7 7.0 - - - +
357B LEU* 1.3 77.9 - - - +
359B LYS* 1.3 63.2 + - - +
361B VAL* 3.4 0.5 + - - +
362B ILE* 3.0 41.2 + - + +
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Residues in contact with LYS 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322A ASP* 6.2 0.2 - - - -
355B GLN 3.0 14.6 + - - +
356B SER* 3.1 9.8 + - - +
358B ARG* 1.3 79.7 - - - +
360B MET* 1.3 57.7 + - + +
362B ILE* 3.3 6.8 + - + +
363B ASP* 2.9 51.2 + - - +
400B TYR* 3.8 29.7 - - + +
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Residues in contact with MET 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285B LEU* 3.9 33.0 - - + +
286B GLU* 3.9 30.5 - - + +
289B ALA* 3.9 10.8 - - + -
356B SER* 2.9 35.9 + - - +
357B LEU* 3.9 9.2 - - - +
359B LYS* 1.3 75.2 - - + +
361B VAL* 1.3 58.3 + - - +
363B ASP* 3.1 2.1 + - - +
364B ILE* 2.8 37.8 + - + +
400B TYR* 3.8 30.5 - - + +
404B ILE* 3.9 18.4 - - + -
407B LEU* 5.0 3.6 - - - -
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Residues in contact with VAL 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289B ALA* 3.8 29.2 - - + +
292B PHE* 3.8 20.9 - - + -
293B ALA* 4.2 14.1 - - + -
296B ILE* 4.0 15.0 - - + -
331B LEU* 3.8 11.4 - - + -
335B PHE* 3.5 24.9 - - + -
357B LEU* 2.8 28.9 + - + +
360B MET* 1.3 76.8 - - - +
362B ILE* 1.3 59.7 + - - +
364B ILE* 3.9 1.0 - - - +
365B VAL* 3.0 25.5 + - - +
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Residues in contact with ILE 362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321A ASN* 3.7 51.4 - - + +
322A ASP* 4.2 5.2 - - + +
323A SER* 5.0 1.8 - - - +
331B LEU* 3.7 9.1 - - + +
335B PHE* 3.7 16.6 - - + -
358B ARG* 3.0 48.1 + - + +
359B LYS* 3.7 7.0 - - + +
361B VAL* 1.3 75.6 - - - +
363B ASP* 1.3 68.8 + - - +
366B LEU* 3.0 42.0 + - + +
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Residues in contact with ASP 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359B LYS* 2.9 37.1 + - - +
360B MET 3.6 3.8 - - - +
362B ILE* 1.3 82.7 - - - +
364B ILE* 1.3 62.1 + - - +
366B LEU* 4.2 6.1 - - - +
367B ALA* 3.5 12.3 + - - +
400B TYR* 2.9 24.3 + - - -
404B ILE* 4.1 13.4 - - + +
408B GLN* 3.0 26.9 - - - +
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Residues in contact with ILE 364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289B ALA 4.5 1.3 - - - -
290B ALA* 4.0 28.5 - - + +
293B ALA* 3.8 14.4 - - + -
360B MET* 2.8 27.3 + - + +
361B VAL 3.9 2.9 - - - +
363B ASP* 1.3 74.4 - - - +
365B VAL* 1.3 66.3 + - - +
367B ALA* 2.9 18.9 + - - +
368B THR* 3.5 7.1 + - - +
404B ILE* 4.2 12.1 - - + -
407B LEU* 4.1 27.8 - - + +
408B GLN* 4.0 14.3 - - + +
411B VAL* 3.5 36.5 - - + +
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Residues in contact with VAL 365 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293B ALA* 3.7 31.9 - - + +
296B ILE* 4.4 3.6 - - + -
297B HIS* 4.1 26.7 - - + +
327B GLU* 3.8 16.9 - - + +
330B HIS* 4.5 3.8 - - + -
331B LEU* 3.6 32.3 - - + +
361B VAL* 3.0 19.6 + - + +
364B ILE* 1.3 76.3 - - + +
366B LEU* 1.3 60.9 + - - +
368B THR* 2.6 33.1 + - - +
411B VAL* 6.2 0.2 - - - -
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Residues in contact with LEU 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321A ASN* 5.2 1.1 - - + -
323A SER* 4.9 10.5 - - - +
324B SER* 4.3 7.4 - - - +
327B GLU* 4.2 8.1 - - + -
328B ASN* 3.9 42.2 - - - +
331B LEU* 3.7 14.8 - - + -
362B ILE* 3.0 38.2 + - + +
363B ASP* 4.3 5.6 - - - +
365B VAL* 1.3 75.8 - - - +
367B ALA* 1.3 59.8 + - - +
369B ASP* 3.5 11.7 - - - +
372B LYS* 3.4 26.4 - - - +
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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