Contacts of the helix formed by residues 350 - 367 (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 THR 350 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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348D ASN 4.1 1.1 + - - +
349D LEU* 1.3 77.1 - - - +
351D LYS* 1.3 64.8 + - - +
352D LYS* 3.2 26.4 - - - +
353D GLN* 2.9 43.6 + - + +
354D ARG* 2.9 19.6 + - - +
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Residues in contact with LYS 351 (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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311C ASN 5.8 4.6 + - - -
449C MET* 6.3 1.2 - - - +
349D LEU 3.7 0.6 + - - -
350D THR* 1.3 71.8 - - - +
352D LYS* 1.3 74.4 + - + +
354D ARG* 3.3 15.6 + - - +
355D GLN* 3.0 51.1 + - + +
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Residues in contact with LYS 352 (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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350D THR* 3.1 23.5 - - - +
351D LYS* 1.3 98.5 - - + +
353D GLN* 1.3 62.1 + - + +
355D GLN* 3.2 16.2 + - - +
356D SER* 3.0 26.1 + - - -
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Residues in contact with GLN 353 (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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232D PHE* 4.3 21.0 - - - -
285D LEU* 3.7 27.3 - - + +
348D ASN 4.7 0.9 - - - +
349D LEU* 3.4 20.3 - - + +
350D THR* 2.9 48.2 + - + +
352D LYS* 1.3 74.3 - - + +
354D ARG* 1.3 60.8 + - - +
356D SER* 3.2 1.8 + - - -
357D LEU* 2.9 32.4 + - - +
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Residues in contact with ARG 354 (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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344D ASP* 3.6 18.4 + - - -
346D PHE* 2.6 45.5 + - + +
347D GLN* 3.5 9.9 + - - +
349D LEU* 3.5 29.8 - - + +
350D THR 2.9 15.8 + - - +
351D LYS* 3.6 14.4 - - - +
353D GLN* 1.3 75.6 - - - +
355D GLN* 1.3 63.0 + - + +
357D LEU* 3.9 7.4 - - - +
358D ARG* 3.0 24.4 + - - +
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Residues in contact with GLN 355 (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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311C ASN* 5.4 4.5 - - - +
351D LYS* 3.0 45.4 + - + +
352D LYS* 3.4 15.2 + - - +
353D GLN 3.1 0.2 - - - -
354D ARG* 1.3 79.8 - - + +
356D SER* 1.3 61.7 + - - +
358D ARG* 3.4 6.7 + - - +
359D LYS* 3.0 23.2 + - - +
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Residues in contact with SER 356 (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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285D LEU* 3.8 17.6 - - - +
352D LYS 3.0 13.7 + - - -
353D GLN* 3.7 6.5 - - - -
355D GLN* 1.3 72.4 - - - +
357D LEU* 1.3 67.2 + - - +
359D LYS* 3.1 7.3 + - - +
360D MET* 2.9 37.4 + - - +
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Residues in contact with LEU 357 (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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285D LEU* 3.8 14.4 - - + +
288D LEU* 3.6 37.7 - - + -
289D ALA* 3.8 16.6 - - - +
292D PHE* 4.7 1.8 - - + -
335D PHE* 5.3 3.4 - - + -
346D PHE* 3.4 41.5 - - + -
349D LEU* 4.9 1.6 - - + -
353D GLN 2.9 17.1 + - - +
354D ARG* 3.9 6.1 - - - +
356D SER* 1.3 78.0 - - - +
358D ARG* 1.3 58.4 + - - +
360D MET* 3.8 10.1 - - - +
361D VAL* 2.9 48.7 + - + +
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Residues in contact with ARG 358 (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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313C ASN* 6.2 0.4 - - - -
317C ALA 3.2 25.3 + - - -
318C LEU* 3.5 21.6 + - - +
321C ASN* 3.7 10.9 + - - +
322C ASP* 3.1 27.6 + - - +
335D PHE* 3.2 62.1 - - + +
354D ARG 3.0 18.7 + - - +
355D GLN* 3.7 6.5 - - - +
356D SER 3.2 0.2 - - - -
357D LEU* 1.3 77.0 - - - +
359D LYS* 1.3 64.1 + - - +
361D VAL* 3.8 0.7 - - - +
362D ILE* 3.0 39.2 + - + +
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Residues in contact with LYS 359 (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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322C ASP* 5.9 1.8 - - - +
355D GLN 3.0 13.8 + - - +
356D SER* 3.1 10.5 + - - +
358D ARG* 1.3 79.5 - - - +
360D MET* 1.3 57.8 + - + +
362D ILE* 3.6 6.7 - - - +
363D ASP* 2.9 51.4 + - - +
400D TYR* 3.7 30.9 - - + +
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Residues in contact with MET 360 (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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285D LEU* 3.9 32.1 - - + +
286D GLU* 3.9 31.0 - - + +
289D ALA* 3.9 10.8 - - + -
356D SER* 2.9 36.4 + - - +
357D LEU* 3.8 10.1 - - - +
359D LYS* 1.3 75.2 - - + +
361D VAL* 1.3 58.1 + - - +
363D ASP* 3.2 1.6 + - - +
364D ILE* 2.8 38.2 + - + +
400D TYR* 3.8 30.5 - - + +
404D ILE* 3.9 18.8 - - + -
407D LEU* 4.9 4.0 - - - -
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Residues in contact with VAL 361 (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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289D ALA* 3.7 29.2 - - - +
292D PHE* 3.8 20.6 - - + -
293D ALA* 4.2 14.4 - - + -
296D ILE* 4.1 14.4 - - + -
331D LEU* 3.8 11.0 - - + -
335D PHE* 3.5 24.9 - - + -
357D LEU* 2.9 28.3 + - + +
360D MET* 1.3 75.0 - - - +
362D ILE* 1.3 64.1 + - - +
364D ILE* 3.3 0.6 + - - -
365D VAL* 3.0 25.5 + - + +
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Residues in contact with ILE 362 (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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321C ASN* 3.4 53.2 - - + +
322C ASP* 4.0 5.8 - - + +
323C SER* 4.4 2.7 - - - +
331D LEU* 3.7 10.3 - - + +
335D PHE* 3.7 16.6 - - + -
358D ARG* 3.0 46.0 + - + +
359D LYS* 3.6 6.5 - - - +
361D VAL* 1.3 75.2 - - - +
363D ASP* 1.3 68.1 + - - +
366D LEU* 3.0 41.6 + - + +
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Residues in contact with ASP 363 (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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359D LYS* 2.9 36.6 + - - +
360D MET 3.6 4.3 - - - +
362D ILE* 1.3 84.1 - - - +
364D ILE* 1.3 63.5 + - - +
366D LEU* 4.3 5.8 - - - +
367D ALA* 3.5 12.1 + - - +
400D TYR* 2.9 24.4 + - - -
404D ILE* 4.1 12.6 - - + +
408D GLN* 3.1 27.1 - - - +
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Residues in contact with ILE 364 (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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289D ALA* 4.5 2.0 - - + -
290D ALA* 3.9 29.2 - - + +
293D ALA* 3.9 13.9 - - + -
360D MET* 2.8 27.1 + - + +
361D VAL 3.8 3.4 - - - +
363D ASP* 1.3 75.2 - - - +
365D VAL* 1.3 61.7 + - + +
367D ALA* 2.9 24.9 + - - +
368D THR* 3.5 6.2 + - - +
404D ILE* 4.2 12.3 - - + -
407D LEU* 4.0 30.5 - - + +
408D GLN* 4.0 12.1 - - + +
411D VAL* 3.6 36.1 - - + -
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Residues in contact with VAL 365 (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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293D ALA* 3.8 33.0 - - + +
296D ILE* 4.4 3.4 - - + -
297D HIS* 4.2 25.8 - - + +
327D GLU* 3.8 17.4 - - + +
330D HIS* 4.5 3.8 - - + -
331D LEU* 3.5 35.9 - - + +
361D VAL* 3.0 14.9 + - + +
364D ILE* 1.3 75.1 - - + +
366D LEU* 1.3 61.4 + - - +
368D THR* 2.6 33.2 + - - +
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Residues in contact with LEU 366 (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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321C ASN* 5.2 0.7 - - + -
323C SER* 4.3 14.4 - - - +
324D SER* 4.3 7.2 - - - +
327D GLU* 4.2 7.2 - - + -
328D ASN* 3.9 39.9 - - - +
331D LEU* 3.7 17.5 - - + -
362D ILE* 3.0 38.7 + - + +
363D ASP* 4.3 7.0 - - - +
365D VAL* 1.3 77.1 - - - +
367D ALA* 1.3 58.6 + - - +
369D ASP* 3.4 20.2 - - - +
372D LYS* 3.5 17.8 - - - +
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Residues in contact with ALA 367 (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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363D ASP 3.5 12.6 + - - +
364D ILE 2.9 13.7 + - - +
366D LEU* 1.3 77.1 - - - +
368D THR* 1.3 58.3 + - - +
369D ASP 3.1 12.2 + - - +
372D LYS* 4.7 9.7 - - - +
376D LEU* 3.6 32.3 - - + +
408D GLN* 3.7 26.0 - - + +
412D HIS* 3.9 8.4 + - - -
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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