Contacts of the helix formed by residues 350 - 366 (chain K) 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 K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348K ASN 4.1 1.3 + - - +
349K LEU* 1.3 75.3 - - - +
351K LYS* 1.3 65.0 + - - +
352K LYS* 3.3 25.3 - - - +
353K GLN* 2.9 43.7 + - + +
354K ARG* 2.9 19.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 351 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349K LEU 3.7 0.6 + - - -
350K THR* 1.3 72.9 - - - +
352K LYS* 1.3 73.8 + - + +
354K ARG* 3.3 14.5 + - - +
355K GLN* 3.1 49.4 + - + +
311L ASN 5.9 2.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 352 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350K THR* 3.1 22.4 - - - +
351K LYS* 1.3 98.8 - - + +
353K GLN* 1.3 63.5 + - + +
355K GLN* 3.2 15.9 + - - +
356K SER* 3.0 26.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 353 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232K PHE* 4.3 20.5 - - - -
285K LEU* 3.7 29.0 - - + +
348K ASN 4.7 0.5 - - - +
349K LEU* 3.4 21.7 - - + +
350K THR* 2.9 50.4 + - + +
352K LYS* 1.3 74.0 - - + +
354K ARG* 1.3 61.0 - - - +
356K SER* 3.3 1.4 + - - -
357K LEU* 2.9 32.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 354 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344K ASP* 3.6 18.6 + - - -
346K PHE* 2.7 45.7 + - + +
347K GLN* 3.5 9.9 + - - +
349K LEU* 3.4 30.5 - - + +
350K THR 2.9 14.6 + - - +
351K LYS* 3.6 14.8 - - - +
353K GLN* 1.3 77.0 - - - +
355K GLN* 1.3 63.0 + - + +
357K LEU* 3.9 6.8 - - - +
358K ARG* 3.1 24.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 355 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351K LYS* 3.1 45.4 + - + +
352K LYS* 3.4 13.9 + - - +
353K GLN 3.2 0.2 - - - -
354K ARG* 1.3 75.2 - - + +
356K SER* 1.3 60.0 + - - +
358K ARG* 3.3 6.5 + - - +
359K LYS* 3.0 28.4 + - - +
311L ASN* 5.5 3.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 356 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285K LEU* 3.9 16.5 - - - +
352K LYS* 3.0 14.5 + - - +
353K GLN* 3.3 6.7 + - - -
355K GLN* 1.3 72.5 - - - +
357K LEU* 1.3 67.4 + - - +
359K LYS* 3.1 6.7 + - - +
360K MET* 2.9 38.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 357 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285K LEU* 3.8 14.1 - - + -
288K LEU* 3.5 37.5 - - + -
289K ALA* 3.8 17.3 - - + +
292K PHE* 4.7 1.8 - - + -
335K PHE* 5.3 3.6 - - + -
346K PHE* 3.4 41.5 - - + -
349K LEU* 4.7 1.3 - - + -
353K GLN 2.9 17.7 + - - +
354K ARG* 3.9 6.3 - - - +
356K SER* 1.3 78.3 - - - +
358K ARG* 1.3 59.5 + - - +
360K MET* 3.4 9.2 + - - +
361K VAL* 2.8 48.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 358 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335K PHE* 3.2 61.3 - - + +
354K ARG 3.1 18.1 + - - +
355K GLN* 3.7 6.3 - - - +
357K LEU* 1.3 77.6 - - + +
359K LYS* 1.3 64.0 + - - +
361K VAL* 3.8 0.7 - - - +
362K ILE* 3.0 39.2 + - + +
317L ALA 3.3 25.3 + - - -
318L LEU* 3.7 18.3 + - - +
321L ASN* 3.6 13.3 + - - +
322L ASP* 3.0 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 359 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355K GLN 3.0 14.4 + - - +
356K SER* 3.5 9.6 - - - +
358K ARG* 1.3 78.2 - - - +
360K MET* 1.3 58.6 + - + +
362K ILE* 3.3 8.3 + - + +
363K ASP* 2.9 50.3 + - - +
400K TYR* 3.7 31.0 - - + +
322L ASP* 6.0 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 360 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285K LEU* 3.9 25.1 - - + +
286K GLU* 3.9 31.4 - - + +
289K ALA* 3.9 17.5 - - + -
356K SER* 2.9 39.9 + - - +
357K LEU* 3.9 9.6 - - - +
359K LYS* 1.3 72.2 - - + +
361K VAL* 1.3 58.2 + - - +
363K ASP* 3.2 1.7 + - - +
364K ILE* 2.8 38.3 + - + +
400K TYR* 3.8 30.1 - - + +
404K ILE* 3.9 17.9 - - + -
407K LEU* 5.0 3.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 361 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289K ALA* 3.8 28.7 - - + +
292K PHE* 3.8 27.6 - - + -
293K ALA* 4.2 14.1 - - + -
296K ILE* 4.1 8.3 - - + -
331K LEU* 3.8 11.0 - - + -
335K PHE* 3.5 26.0 - - + -
357K LEU* 2.8 33.1 + - + +
360K MET* 1.3 71.9 - - - +
362K ILE* 1.3 56.9 + - - +
364K ILE* 3.8 0.8 - - - +
365K VAL* 2.9 31.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 362 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331K LEU* 3.7 10.7 - - + +
335K PHE* 3.7 15.5 - - + -
358K ARG* 3.0 47.0 + - + +
359K LYS* 3.6 5.6 - - + +
361K VAL* 1.3 75.2 - - - +
363K ASP* 1.3 68.6 - - - +
366K LEU* 3.0 45.6 + - + +
321L ASN* 3.3 50.5 - - + +
322L ASP* 4.1 5.2 - - + +
323L SER* 4.3 2.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 363 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359K LYS* 2.9 36.8 + - - +
360K MET 3.6 3.4 - - - +
362K ILE* 1.3 85.2 - - - +
364K ILE* 1.3 63.0 + - - +
366K LEU* 3.8 6.1 + - - +
367K ALA* 3.5 12.3 + - - +
400K TYR* 2.9 23.6 + - - -
404K ILE* 4.0 13.5 - - + +
408K GLN* 3.1 26.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 364 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289K ALA 4.4 0.9 - - - -
290K ALA* 3.9 28.7 - - + +
293K ALA* 3.9 13.9 - - + -
360K MET* 2.8 27.9 + - + +
361K VAL 3.8 2.7 - - - +
363K ASP* 1.3 74.0 - - - +
365K VAL* 1.3 62.3 + - + +
367K ALA* 2.9 24.6 + - - +
368K THR* 3.5 6.4 + - - +
404K ILE* 4.2 11.7 - - + -
407K LEU* 4.0 29.4 - - + +
408K GLN* 3.9 14.4 - - + +
411K VAL* 3.5 36.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 365 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293K ALA* 3.7 33.2 - - + +
296K ILE* 4.4 3.6 - - + -
297K HIS* 4.1 27.4 - - + +
327K GLU* 3.8 17.4 - - + +
330K HIS* 4.5 2.9 - - + -
331K LEU* 3.5 35.9 - - + +
361K VAL* 2.9 18.6 + - + +
364K ILE* 1.3 75.8 - - + +
366K LEU* 1.3 60.8 + - - +
368K THR* 2.6 33.8 + - - +
411K VAL* 6.5 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 366 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324K SER* 4.3 8.1 - - - -
327K GLU* 4.2 6.7 - - + -
328K ASN* 3.8 39.7 - - - +
331K LEU* 3.7 17.5 - - + -
362K ILE* 3.0 39.1 + - + +
363K ASP* 4.2 6.3 - - - +
364K ILE 3.2 0.2 - - - -
365K VAL* 1.3 76.7 - - - +
367K ALA* 1.3 58.9 + - - +
368K THR 3.2 1.2 + - - -
369K ASP* 3.5 11.4 - - - +
372K LYS* 3.4 26.7 - - - +
321L ASN* 5.3 0.7 - - + -
323L SER* 4.3 14.6 - - - +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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