Contacts of the helix formed by residues 350 - 366 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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348L ASN 4.1 1.1 + - - +
349L LEU* 1.3 77.1 - - - +
351L LYS* 1.3 64.4 + - - +
352L LYS* 3.3 25.1 - - - +
353L GLN* 2.9 43.0 + - - +
354L ARG* 2.9 18.0 + - - +
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Residues in contact with LYS 351 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311K ASN* 5.8 6.1 + - - +
449K MET* 6.0 4.6 - - - +
349L LEU 3.6 0.8 + - - -
350L THR* 1.3 73.5 - - - +
352L LYS* 1.3 74.8 + - + +
354L ARG* 3.4 14.2 + - + +
355L GLN* 3.1 50.0 + - + +
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Residues in contact with LYS 352 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350L THR* 3.1 22.6 - - - +
351L LYS* 1.3 98.8 - - + +
353L GLN* 1.3 57.8 + - + +
355L GLN* 3.2 15.7 + - - +
356L SER* 3.0 31.7 + - - -
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Residues in contact with GLN 353 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232L PHE* 4.3 19.9 - - - -
285L LEU* 3.7 27.5 - - + +
348L ASN 4.7 0.9 - - - +
349L LEU* 3.4 21.3 - - + +
350L THR* 2.9 50.5 + - - +
352L LYS* 1.3 73.6 - - + +
354L ARG* 1.3 60.1 - - - +
356L SER* 3.2 1.6 + - - -
357L LEU* 2.8 32.5 + - - +
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Residues in contact with ARG 354 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344L ASP* 3.6 18.3 + - - -
346L PHE* 2.6 45.8 + - + +
347L GLN* 3.5 9.8 + - - +
349L LEU* 3.4 29.4 - - + +
350L THR 2.9 15.0 + - - +
351L LYS* 3.6 16.4 - - + +
353L GLN* 1.3 75.8 - - - +
355L GLN* 1.3 59.8 + - + +
357L LEU* 3.5 6.8 + - - +
358L ARG* 3.0 30.0 + - - +
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Residues in contact with GLN 355 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311K ASN* 5.0 8.9 - - - +
351L LYS* 3.1 45.6 + - + +
352L LYS* 3.5 14.3 - - - +
354L ARG* 1.3 77.0 - - + +
356L SER* 1.3 62.0 + - - +
358L ARG* 3.4 6.4 + - - +
359L LYS* 3.0 23.8 + - - +
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Residues in contact with SER 356 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285L LEU* 3.8 17.4 - - - +
352L LYS* 3.0 14.9 + - - +
353L GLN 3.7 6.5 - - - -
355L GLN* 1.3 73.5 - - - +
357L LEU* 1.3 66.5 + - - +
359L LYS* 3.1 6.1 + - - +
360L MET* 2.8 37.1 + - - +
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Residues in contact with LEU 357 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285L LEU* 3.9 13.2 - - + -
288L LEU* 3.6 36.6 - - + -
289L ALA* 3.7 18.4 - - + +
292L PHE* 4.6 1.6 - - + -
335L PHE* 5.2 3.8 - - + -
346L PHE* 3.4 41.5 - - + -
349L LEU* 4.7 2.0 - - + -
353L GLN 2.8 18.1 + - - +
354L ARG* 3.8 6.5 - - - +
356L SER* 1.3 77.7 - - - +
358L ARG* 1.3 60.2 + - - +
360L MET* 3.8 9.4 - - - +
361L VAL* 2.8 48.1 + - + +
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Residues in contact with ARG 358 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310K ILE* 5.6 0.4 - - - +
317K ALA 3.2 17.4 + - - -
318K LEU* 4.0 12.8 + - - +
321K ASN* 3.4 12.1 + - - +
322K ASP* 2.5 44.6 + - - +
335L PHE* 3.2 60.7 - - + +
354L ARG 3.0 18.1 + - - +
355L GLN* 3.7 6.7 - - - +
357L LEU* 1.3 77.0 - - - +
359L LYS* 1.3 63.4 + - - +
361L VAL* 3.8 0.9 - - - +
362L ILE* 3.0 39.8 + - + +
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Residues in contact with LYS 359 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322K ASP* 6.0 0.2 - - - -
355L GLN 3.0 14.4 + - - +
356L SER* 3.6 9.0 - - - +
358L ARG* 1.3 78.0 - - - +
360L MET* 1.3 57.6 + - + +
362L ILE* 3.3 8.0 + - + +
363L ASP* 2.9 52.1 + - - +
400L TYR* 3.7 30.3 - - + +
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Residues in contact with MET 360 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285L LEU* 3.9 24.9 - - + +
286L GLU* 3.9 31.6 - - + +
289L ALA* 3.9 17.0 - - + -
356L SER* 2.8 41.2 + - - +
357L LEU* 3.9 9.2 - - - +
359L LYS* 1.3 71.8 - - + +
361L VAL* 1.3 57.5 + - - +
363L ASP* 3.2 1.7 + - - +
364L ILE* 2.8 38.6 + - + +
400L TYR* 3.8 29.2 - - + -
404L ILE* 3.9 17.9 - - + -
407L LEU* 5.0 4.3 - - + -
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Residues in contact with VAL 361 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289L ALA* 3.7 29.2 - - + +
292L PHE* 3.8 26.9 - - + -
293L ALA* 4.2 13.2 - - - -
296L ILE* 4.1 8.7 - - + -
331L LEU* 3.8 11.4 - - + -
335L PHE* 3.5 25.4 - - + -
357L LEU* 2.8 31.9 + - + +
360L MET* 1.3 71.4 - - - +
362L ILE* 1.3 56.0 + - - +
364L ILE* 3.3 1.5 + - - +
365L VAL* 2.9 31.0 + - - +
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Residues in contact with ILE 362 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321K ASN* 3.1 44.2 - - + +
322K ASP* 3.9 6.5 - - + +
323K SER* 4.1 4.0 - - - +
331L LEU* 3.7 14.7 - - + +
335L PHE* 3.7 16.2 - - + -
358L ARG* 3.0 45.4 + - + +
359L LYS* 3.7 7.4 - - + +
361L VAL* 1.3 74.7 - - - +
363L ASP* 1.3 69.1 + - - +
366L LEU* 3.0 45.6 + - + +
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Residues in contact with ASP 363 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359L LYS* 2.9 37.6 + - - +
360L MET 3.2 3.3 + - - +
362L ILE* 1.3 82.0 - - - +
364L ILE* 1.3 63.1 + - - +
366L LEU* 3.9 6.5 + - - +
367L ALA* 3.5 12.5 + - - +
400L TYR* 2.9 24.4 + - - -
404L ILE* 4.1 13.2 - - + +
408L GLN* 3.1 26.4 - - - +
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Residues in contact with ILE 364 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289L ALA 4.4 1.3 - - - -
290L ALA* 3.9 28.0 - - - +
293L ALA* 3.9 14.8 - - + -
360L MET* 2.8 27.8 + - + +
361L VAL 3.8 2.7 - - - +
363L ASP* 1.3 74.9 - - - +
365L VAL* 1.3 61.9 + - - +
367L ALA* 2.9 24.6 + - - +
368L THR* 3.5 6.6 + - - +
404L ILE* 4.1 12.8 - - + -
407L LEU* 4.0 30.7 - - + +
408L GLN* 3.9 13.1 - - + +
411L VAL* 3.5 36.8 - - + -
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Residues in contact with VAL 365 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293L ALA* 3.8 32.8 - - + +
296L ILE* 4.4 4.0 - - + +
297L HIS* 4.1 26.7 - - + +
327L GLU* 3.8 17.7 - - + +
330L HIS* 4.5 3.6 - - + -
331L LEU* 3.5 36.8 - - + +
361L VAL* 2.9 21.6 + - + +
364L ILE* 1.3 73.4 - - + +
366L LEU* 1.3 62.0 + - - +
368L THR* 2.7 32.4 + - - +
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Residues in contact with LEU 366 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321K ASN* 5.7 0.4 - - + -
323K SER* 4.2 14.1 - - - +
324L SER* 4.3 7.4 - - - +
327L GLU* 4.2 7.2 - - + -
328L ASN* 3.8 42.0 - - - +
331L LEU* 3.7 15.7 - - + -
362L ILE* 3.0 37.8 + - + +
363L ASP* 4.3 6.5 - - - +
365L VAL* 1.3 75.4 - - - +
367L ALA* 1.3 59.2 + - - +
368L THR 3.2 0.4 - - - -
369L ASP* 3.5 12.2 - - - +
372L LYS* 3.4 26.6 - - + +
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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