Contacts of the helix formed by residues 350 - 366 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348C ASN 4.1 1.5 + - - +
349C LEU* 1.3 75.7 - - - +
351C LYS* 1.3 65.4 + - - +
352C LYS* 3.3 26.3 - - - +
353C GLN* 2.9 42.2 + - - +
354C ARG* 2.9 18.2 + - - +
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Residues in contact with LYS 351 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349C LEU 3.7 0.8 + - - -
350C THR* 1.3 73.3 - - - +
352C LYS* 1.3 74.0 + - + +
354C ARG* 3.4 15.0 + - - +
355C GLN* 3.1 49.4 + - + +
311D ASN* 5.8 4.1 + - - +
449D MET* 6.1 2.8 - - - +
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Residues in contact with LYS 352 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350C THR* 3.1 23.3 - - - +
351C LYS* 1.3 99.4 - - + +
353C GLN* 1.3 61.5 + - + +
355C GLN* 3.2 16.5 + - - +
356C SER* 3.0 26.9 + - - -
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Residues in contact with GLN 353 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232C PHE* 4.3 20.7 - - - -
285C LEU* 3.8 28.1 - - + +
348C ASN 4.7 0.7 - - - +
349C LEU* 3.4 19.6 - - + +
350C THR* 2.9 48.2 + - + +
352C LYS* 1.3 74.4 - - + +
354C ARG* 1.3 61.0 - - - +
356C SER* 3.2 2.0 + - - -
357C LEU* 2.9 32.2 + - - +
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Residues in contact with ARG 354 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344C ASP* 3.6 18.2 + - - -
346C PHE* 2.6 46.9 + - + +
347C GLN* 3.5 10.5 + - - +
349C LEU* 3.5 30.1 - - + +
350C THR 2.9 15.0 + - - +
351C LYS* 3.6 14.8 - - - +
352C LYS 3.3 0.2 - - - -
353C GLN* 1.3 74.5 - - - +
355C GLN* 1.3 64.5 + - + +
357C LEU* 3.9 6.6 - - - +
358C ARG* 3.0 25.3 + - - +
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Residues in contact with GLN 355 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351C LYS* 3.1 45.0 + - + +
352C LYS* 3.4 14.3 + - - +
353C GLN 3.2 0.2 - - - -
354C ARG* 1.3 77.4 - - + +
356C SER* 1.3 61.8 + - - +
358C ARG* 3.4 6.9 + - - +
359C LYS* 3.0 23.2 + - - +
311D ASN* 5.1 7.1 - - - +
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Residues in contact with SER 356 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285C LEU* 3.9 16.9 - - - +
352C LYS* 3.0 14.9 + - - +
353C GLN 3.7 6.5 - - - -
355C GLN* 1.3 72.1 - - - +
357C LEU* 1.3 67.2 + - - +
359C LYS* 3.1 6.3 + - - +
360C MET* 2.9 37.5 + - - +
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Residues in contact with LEU 357 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285C LEU* 3.8 13.2 - - + +
288C LEU* 3.6 36.1 - - + -
289C ALA* 3.7 18.4 - - + +
292C PHE* 4.7 2.0 - - + -
335C PHE* 5.3 3.4 - - + -
346C PHE* 3.4 41.7 - - + -
349C LEU* 4.7 2.7 - - + -
353C GLN 2.9 17.7 + - - +
354C ARG* 3.9 6.3 - - - +
356C SER* 1.3 75.8 - - - +
358C ARG* 1.3 62.2 + - - +
360C MET* 3.8 9.9 - - - +
361C VAL* 2.9 47.6 + - + +
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Residues in contact with ARG 358 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335C PHE* 3.2 61.7 - - + +
354C ARG 3.0 18.2 + - - +
355C GLN* 3.7 6.3 - - - +
357C LEU* 1.3 77.0 - - + +
359C LYS* 1.3 63.9 + - - +
361C VAL* 3.9 0.5 - - - +
362C ILE* 3.0 40.1 + - + +
317D ALA 3.2 18.0 + - - -
318D LEU* 3.8 14.0 + - - +
321D ASN* 3.5 11.9 + - - +
322D ASP* 2.7 41.1 + - - +
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Residues in contact with LYS 359 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355C GLN 3.0 14.4 + - - +
356C SER* 3.1 9.6 + - - +
358C ARG* 1.3 77.2 - - - +
360C MET* 1.3 63.1 + - + +
362C ILE* 3.3 7.0 + - + +
363C ASP* 2.9 46.6 + - - +
400C TYR* 3.7 30.6 - - + +
322D ASP* 6.1 0.2 - - - -
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Residues in contact with MET 360 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285C LEU* 4.0 31.4 - - + +
286C GLU* 3.9 31.4 - - + +
289C ALA* 3.9 11.0 - - + -
356C SER* 2.9 36.8 + - - +
357C LEU* 3.8 10.5 - - - +
359C LYS* 1.3 76.5 - - + +
361C VAL* 1.3 56.9 + - - +
363C ASP* 3.2 2.1 + - - +
364C ILE* 2.8 37.9 + - + +
400C TYR* 3.8 28.9 - - + +
404C ILE* 3.9 17.7 - - + -
407C LEU* 5.0 3.6 - - - -
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Residues in contact with VAL 361 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289C ALA* 3.7 29.4 - - - +
292C PHE* 3.8 19.5 - - + -
293C ALA* 4.2 13.5 - - + -
296C ILE* 4.1 15.3 - - + -
331C LEU* 3.7 11.0 - - + -
335C PHE* 3.5 25.1 - - + -
357C LEU* 2.9 28.7 + - + +
360C MET* 1.3 75.7 - - - +
362C ILE* 1.3 62.7 + - - +
364C ILE* 3.3 1.1 + - - +
365C VAL* 2.9 25.3 + - - +
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Residues in contact with ILE 362 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331C LEU* 3.7 13.9 - - + +
335C PHE* 3.7 15.7 - - + -
358C ARG* 3.0 45.7 + - + +
359C LYS* 3.7 6.5 - - + +
361C VAL* 1.3 75.8 - - - +
363C ASP* 1.3 68.6 + - - +
366C LEU* 3.0 46.2 + - + +
321D ASN* 3.2 44.0 - - + +
322D ASP* 4.0 6.3 - - + +
323D SER* 4.3 2.9 - - - +
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Residues in contact with ASP 363 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359C LYS* 2.9 37.0 + - - +
360C MET 3.6 4.0 - - - +
362C ILE* 1.3 86.5 - - - +
364C ILE* 1.3 61.6 + - - +
366C LEU* 4.3 5.4 - - - +
367C ALA* 3.5 12.0 + - - +
400C TYR* 2.9 23.9 + - - -
404C ILE* 4.1 13.4 - - + +
408C GLN* 3.0 27.7 - - - +
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Residues in contact with ILE 364 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289C ALA* 4.5 1.1 - - + -
290C ALA* 3.9 28.9 - - + +
293C ALA* 3.8 14.4 - - + -
360C MET* 2.8 26.6 + - + +
361C VAL 3.8 2.9 - - - +
363C ASP* 1.3 75.7 - - - +
365C VAL* 1.3 67.2 + - - +
367C ALA* 2.9 18.4 + - - +
368C THR* 3.5 6.8 + - - +
404C ILE* 4.2 11.9 - - + -
407C LEU* 4.0 28.9 - - + +
408C GLN* 3.9 14.8 - - + +
411C VAL* 3.5 36.6 - - + -
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Residues in contact with VAL 365 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293C ALA* 3.8 33.2 - - + +
296C ILE* 4.4 3.6 - - + +
297C HIS* 4.2 26.5 - - + +
327C GLU* 3.8 17.8 - - + +
330C HIS* 4.5 3.4 - - + -
331C LEU* 3.5 37.0 - - + +
361C VAL* 2.9 17.6 + - + +
364C ILE* 1.3 74.4 - - - +
366C LEU* 1.3 58.5 + - - +
368C THR* 2.6 35.9 + - - +
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Residues in contact with LEU 366 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324C SER* 4.3 7.4 + - - +
327C GLU* 4.1 8.5 - - + -
328C ASN* 3.9 39.7 - - - +
331C LEU* 3.7 17.5 - - + -
362C ILE* 3.0 38.8 + - + +
363C ASP* 4.3 5.8 - - - +
365C VAL* 1.3 76.1 - - - +
367C ALA* 1.3 59.6 + - - +
369C ASP* 3.5 11.3 - - - +
372C LYS* 3.4 26.1 - - - +
321D ASN* 5.6 0.7 - - + -
323D SER* 4.4 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
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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