Contacts of the helix formed by residues 350 - 367 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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348I ASN 4.1 1.1 + - - +
349I LEU* 1.3 74.5 - - - +
351I LYS* 1.3 65.7 + - - +
352I LYS* 3.3 26.4 - - - +
353I GLN* 2.9 42.2 + - - +
354I ARG* 2.9 19.6 + - - +
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Residues in contact with LYS 351 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349I LEU 3.7 0.8 + - - -
350I THR* 1.3 72.8 - - - +
352I LYS* 1.3 73.6 + - + +
354I ARG* 3.4 15.3 + - + +
355I GLN* 3.1 49.8 + - + +
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Residues in contact with LYS 352 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350I THR* 3.1 22.9 - - - +
351I LYS* 1.3 96.6 - - + +
353I GLN* 1.3 62.6 + - + +
355I GLN* 3.2 16.3 + - - +
356I SER* 3.0 26.8 + - - +
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Residues in contact with GLN 353 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232I PHE* 4.3 20.6 - - - -
285I LEU* 3.8 26.4 - - + +
348I ASN 4.8 0.7 - - - +
349I LEU* 3.4 21.7 - - + +
350I THR* 2.9 52.8 + - - +
352I LYS* 1.3 74.1 - - + +
354I ARG* 1.3 60.4 - - - +
356I SER* 3.3 2.2 + - - -
357I LEU* 2.9 31.4 + - - +
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Residues in contact with ARG 354 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344I ASP* 3.6 17.6 + - - -
346I PHE* 2.6 45.6 + - + +
347I GLN* 3.5 9.3 + - - +
349I LEU* 3.5 29.6 - - + +
350I THR 2.9 15.0 + - - +
351I LYS* 3.6 15.5 - - + +
353I GLN* 1.3 75.0 - - - +
355I GLN* 1.3 57.6 + - + +
357I LEU* 3.9 6.7 - - - +
358I ARG* 3.0 29.5 + - - +
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Residues in contact with GLN 355 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351I LYS* 3.1 44.4 + - + +
352I LYS* 3.5 14.8 + - - +
353I GLN 3.2 0.2 - - - -
354I ARG* 1.3 76.2 - - + +
356I SER* 1.3 64.7 + - - +
358I ARG* 3.3 7.7 + - - +
359I LYS* 3.0 22.3 + - - +
311J ASN* 5.5 3.5 - - - +
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Residues in contact with SER 356 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285I LEU* 3.9 16.7 - - - +
352I LYS 3.0 13.4 + - - -
353I GLN* 3.7 6.9 - - - -
355I GLN* 1.3 73.7 - - - +
357I LEU* 1.3 67.6 + - - +
359I LYS* 3.1 7.4 + - - +
360I MET* 2.9 37.2 + - - +
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Residues in contact with LEU 357 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285I LEU* 3.9 13.2 - - + -
288I LEU* 3.5 36.8 - - + -
289I ALA* 3.8 18.4 - - + +
292I PHE* 4.7 1.8 - - + -
335I PHE* 5.3 3.6 - - + -
346I PHE* 3.4 41.3 - - + -
349I LEU* 4.7 1.6 - - + -
353I GLN 2.9 17.9 + - - +
354I ARG* 3.9 5.8 - - - +
356I SER* 1.3 75.6 - - - +
358I ARG* 1.3 67.4 + - - +
360I MET* 3.9 9.1 - - - +
361I VAL* 2.9 42.5 + - + +
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Residues in contact with ARG 358 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335I PHE* 3.2 61.4 - - + +
354I ARG 3.0 19.2 + - - +
355I GLN* 3.7 5.8 - - - +
356I SER 3.2 0.2 - - - -
357I LEU* 1.3 76.0 - - + +
359I LYS* 1.3 64.1 + - - +
361I VAL* 3.9 0.5 - - - +
362I ILE* 3.0 39.6 + - + +
310J ILE* 5.6 0.4 - - - +
317J ALA 3.3 16.0 + - - -
318J LEU* 4.0 12.8 + - - +
321J ASN* 3.7 10.5 + - - +
322J ASP* 2.6 42.4 + - - +
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Residues in contact with LYS 359 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355I GLN 3.0 13.8 + - - +
356I SER* 3.1 10.1 + - - +
358I ARG* 1.3 78.5 - - - +
360I MET* 1.3 57.5 + - + +
362I ILE* 3.6 6.4 - - - +
363I ASP* 2.9 50.9 + - - +
400I TYR* 3.7 31.8 - - + +
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Residues in contact with MET 360 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285I LEU* 3.9 31.2 - - + +
286I GLU* 3.9 30.5 - - + +
289I ALA* 3.9 11.9 - - + -
356I SER* 2.9 40.4 + - - +
357I LEU* 3.9 8.5 - - - +
359I LYS* 1.3 72.9 - - + +
361I VAL* 1.3 57.3 + - - +
363I ASP* 3.2 1.2 + - - +
364I ILE* 2.8 39.0 + - + +
400I TYR* 3.8 29.8 - - + -
404I ILE* 3.9 17.7 - - + -
407I LEU* 5.0 3.6 - - + -
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Residues in contact with VAL 361 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289I ALA* 3.8 28.5 - - - +
292I PHE* 3.8 26.7 - - + -
293I ALA* 4.2 14.1 - - - -
296I ILE* 4.1 8.7 - - + -
331I LEU* 3.8 11.0 - - + -
335I PHE* 3.5 25.1 - - + -
357I LEU* 2.9 29.3 + - + +
360I MET* 1.3 74.9 - - - +
362I ILE* 1.3 63.7 + - - +
364I ILE* 3.2 1.3 + - - +
365I VAL* 2.9 25.2 + - + +
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Residues in contact with ILE 362 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331I LEU* 3.7 10.1 - - + -
335I PHE* 3.7 16.2 - - + -
358I ARG* 3.0 47.0 + - + +
359I LYS* 3.6 6.5 - - + +
361I VAL* 1.3 74.5 - - - +
363I ASP* 1.3 69.0 + - - +
366I LEU* 3.0 45.6 + - + +
321J ASN* 3.3 45.5 - - + +
322J ASP* 3.9 6.3 - - + +
323J SER* 4.2 3.8 - - - +
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Residues in contact with ASP 363 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359I LYS* 2.9 38.5 + - - +
360I MET 3.6 3.4 - - - +
362I ILE* 1.3 82.9 - - - +
364I ILE* 1.3 62.8 + - - +
366I LEU* 4.3 6.1 - - - +
367I ALA* 3.5 12.1 + - - +
400I TYR* 2.9 23.7 + - - -
404I ILE* 4.1 13.3 - - + +
408I GLN* 3.1 27.3 - - - +
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Residues in contact with ILE 364 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289I ALA 4.4 1.1 - - - +
290I ALA* 3.9 28.9 - - + +
293I ALA* 3.9 15.0 - - + -
360I MET* 2.8 27.5 + - + +
361I VAL 3.8 2.7 - - - +
363I ASP* 1.3 75.5 - - - +
365I VAL* 1.3 67.4 + - - +
367I ALA* 2.9 19.1 + - - +
368I THR* 3.5 6.6 + - - +
404I ILE* 4.2 11.4 - - + -
407I LEU* 4.0 30.5 - - + +
408I GLN* 4.0 13.0 - - + +
411I VAL* 3.5 36.1 - - + -
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Residues in contact with VAL 365 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293I ALA* 3.7 33.4 - - + +
296I ILE* 4.4 3.4 - - + -
297I HIS* 4.1 25.4 - - + +
327I GLU* 3.8 16.9 - - + +
330I HIS* 4.5 3.6 - - + -
331I LEU* 3.5 36.6 - - + +
361I VAL* 2.9 17.0 + - + +
364I ILE* 1.3 75.7 - - + +
366I LEU* 1.3 61.5 + - - +
367I ALA 3.0 0.2 - - - -
368I THR* 2.6 32.6 + - - +
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Residues in contact with LEU 366 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324I SER* 4.2 7.8 + - - +
327I GLU* 4.2 15.5 - - + -
328I ASN* 3.9 33.9 - - - +
331I LEU* 3.7 15.3 - - + -
362I ILE* 3.0 37.4 + - + +
363I ASP* 4.3 6.3 - - - +
365I VAL* 1.3 76.5 - - - +
367I ALA* 1.3 59.2 + - - +
368I THR 3.2 0.7 - - - -
369I ASP* 3.4 12.8 - - - +
372I LYS* 3.4 26.3 - - - +
321J ASN* 5.5 0.4 - - + -
323J SER* 4.2 14.1 - - - +
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Residues in contact with ALA 367 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363I ASP 3.5 12.6 + - - +
364I ILE 2.9 13.4 + - - +
366I LEU* 1.3 77.3 - - - +
368I THR* 1.3 58.3 + - - +
369I ASP 3.1 12.0 + - - +
372I LYS* 4.7 8.8 - - - +
376I LEU* 3.5 32.3 - - + +
408I GLN* 3.7 26.9 - - + +
412I HIS* 3.9 8.6 + - - -
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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