Contacts of the helix formed by residues 359 - 377 (chain C) in PDB entry 1M1D
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 359 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A ILE* 3.7 2.0 - - - -
70A LYS* 4.7 6.1 - - - +
82A LYS* 6.6 0.2 - - + -
357C ASP* 2.7 39.2 + - - +
358C GLY* 1.3 79.5 - - - +
360C HIS* 1.3 66.7 + - - +
361C ARG* 4.5 3.3 - - - +
362C ASN* 3.2 18.9 + - - +
363C MET* 3.0 26.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 360 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A LYS* 5.8 7.5 - - + +
67A ILE* 3.8 22.1 - - + +
358C GLY 4.0 0.4 + - - -
359C THR* 1.3 73.6 - - - +
361C ARG* 1.3 71.1 + - + +
363C MET* 4.4 0.5 - - - +
364C LYS* 3.2 51.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 361 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352C ASP* 3.5 22.1 + - - -
354C LEU* 4.0 8.9 - - - +
359C THR* 3.4 3.2 + - - +
360C HIS* 1.3 88.8 - - + +
362C ASN* 1.3 70.8 + - - +
364C LYS* 3.3 6.7 + - - +
365C LEU* 3.0 51.6 + - + +
400C LEU* 3.6 17.4 - - - +
403C LYS* 3.4 25.1 + - - +
404C GLN* 5.1 0.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 362 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353C ILE 5.2 0.9 - - - +
354C LEU* 3.5 29.0 - - + +
355C THR* 3.4 23.3 + - - +
357C ASP* 3.1 27.8 - - - +
359C THR* 3.2 20.8 + - - +
361C ARG* 1.3 88.6 - - - +
363C MET* 1.3 64.5 + - - +
365C LEU* 3.3 3.5 + - - +
366C LEU* 2.9 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 363 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A MET* 3.7 30.7 - - + -
67A ILE* 3.8 9.6 - - + -
90A PHE* 4.6 12.8 - - + -
355C THR 4.4 0.2 - - - +
356C ASN* 3.6 26.5 - - + +
357C ASP* 3.9 2.0 - - - +
358C GLY* 3.5 34.8 - - - -
359C THR 3.0 21.2 + - - +
360C HIS 4.4 0.2 - - - +
362C ASN* 1.3 75.1 - - - +
364C LYS* 1.3 62.2 + - - +
366C LEU* 3.2 7.9 + - + +
367C ILE* 3.0 29.9 + - - +
390C PHE* 3.4 36.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 364 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A HIS* 3.8 26.0 + - + +
63A MET* 5.3 0.6 - - - +
64A LYS* 4.5 18.9 - - - +
360C HIS* 3.2 48.4 + - - +
361C ARG* 3.5 7.4 - - + +
362C ASN 3.2 0.6 - - - -
363C MET* 1.3 77.0 - - - +
365C LEU* 1.3 66.7 + - + +
367C ILE* 3.2 7.2 + - - +
368C ASP* 3.1 29.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 365 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354C LEU* 3.4 25.7 - - + +
361C ARG* 3.0 61.2 + - + +
364C LYS* 1.3 79.2 - - + +
366C LEU* 1.3 60.6 + - - +
368C ASP* 3.2 12.4 + - - +
369C LEU* 2.8 30.0 + - - +
400C LEU* 4.1 10.5 - - + -
404C GLN* 3.6 22.4 - - - +
406C VAL* 3.4 26.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 366 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354C LEU* 4.1 19.7 - - + +
355C THR 4.0 11.7 - - - +
356C ASN* 3.5 30.3 - - - +
362C ASN 2.9 21.2 + - - +
363C MET* 3.5 23.3 - - + +
364C LYS 3.2 0.2 - - - -
365C LEU* 1.3 75.3 - - - +
367C ILE* 1.3 53.6 + - - +
369C LEU* 3.2 7.1 + - + +
370C LYS* 2.7 35.0 + - - +
389C VAL* 4.0 17.9 - - + +
390C PHE* 3.7 13.4 - - + -
396C SER* 4.0 30.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 367 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A GLY 3.2 27.4 - - - +
59A THR* 3.6 7.2 - - - +
60A HIS* 3.4 56.3 - - + +
63A MET* 3.7 18.4 - - + -
363C MET 3.0 21.4 + - - +
364C LYS* 3.2 6.5 + - - +
366C LEU* 1.3 75.0 - - - +
368C ASP* 1.3 58.0 + - - +
370C LYS* 3.1 7.7 + - - +
371C ASN* 2.8 39.0 + - - +
390C PHE* 3.7 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 368 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A HIS* 3.4 22.0 + - - -
364C LYS* 3.1 19.6 + - - +
365C LEU* 3.2 21.0 + - - +
367C ILE* 1.3 75.7 - - - +
369C LEU* 1.3 62.2 + - - +
371C ASN* 3.2 11.8 + - - +
372C ILE* 3.2 26.8 + - + +
404C GLN 5.2 1.9 - - - +
406C VAL* 4.0 16.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 369 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365C LEU 2.8 12.9 + - - +
366C LEU* 3.4 12.8 - - + +
368C ASP* 1.3 76.5 - - - +
370C LYS* 1.3 57.9 + - - +
372C ILE* 3.1 9.4 + - + +
373C PHE* 2.9 70.6 + - + -
389C VAL* 5.3 2.0 - - + -
396C SER* 3.7 29.4 - - - +
398C VAL* 3.7 19.1 - - + -
406C VAL* 4.0 11.2 - - + +
408C GLY* 4.0 4.3 - - - -
409C GLY* 3.9 20.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 370 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A ASP 5.2 0.6 + - - -
58A GLY* 3.3 32.3 + - - -
59A THR* 5.0 4.4 - - - +
366C LEU 2.7 20.8 + - - +
367C ILE* 3.1 10.8 + - - +
369C LEU* 1.3 72.7 - - - +
371C ASN* 1.3 83.9 + - - +
373C PHE* 3.4 13.5 + - - +
374C SER* 3.0 25.5 + - - -
382C LYS* 3.6 22.2 - - + +
385C ILE* 3.8 19.3 - - + +
386C VAL* 3.7 27.4 - - + +
389C VAL* 4.6 5.4 - - + +
390C PHE* 4.2 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 371 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A HIS* 4.8 6.9 + - - -
367C ILE* 2.8 31.8 + - - +
368C ASP* 3.5 11.9 + - - +
369C LEU 3.1 0.2 - - - -
370C LYS* 1.3 100.2 + - - +
372C ILE* 1.3 64.0 + - + +
374C SER* 3.5 5.0 + - - -
375C ARG* 3.2 32.9 + - - +
382C LYS* 2.9 19.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 372 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368C ASP 3.2 11.5 + - - +
369C LEU* 3.1 11.7 + - + +
371C ASN* 1.3 73.6 - - + +
373C PHE* 1.3 68.3 + - - +
375C ARG* 3.1 10.1 + - - +
376C GLN* 2.9 24.4 + - + +
406C VAL* 3.4 45.5 - - + +
407C ILE 4.1 3.4 - - - -
408C GLY* 4.0 8.1 - - - +
427C ALA* 4.3 15.0 - - + +
428C VAL 4.3 4.5 - - - -
429C THR* 4.0 36.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 373 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369C LEU* 2.9 52.5 + - + -
370C LYS* 3.5 9.6 - - - +
372C ILE* 1.3 78.3 - - - +
374C SER* 1.3 57.9 + - - +
376C GLN 3.1 0.3 + - - -
377C LEU* 2.8 39.3 + - + +
385C ILE* 4.0 15.0 - - + -
389C VAL* 3.8 20.0 - - + -
409C GLY 3.5 19.7 - - - -
411C CYS* 3.7 27.4 - - + -
425C PHE* 3.6 34.1 - + + -
426C LEU 3.9 0.7 - - - -
427C ALA* 3.8 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 374 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370C LYS 3.0 16.8 + - - -
371C ASN 3.7 5.4 - - - -
372C ILE 3.2 0.2 - - - -
373C PHE* 1.3 77.4 - - - +
375C ARG* 1.3 64.2 + - - +
377C LEU 3.4 15.9 - - - +
378C PRO* 3.7 4.2 - - - +
380C MET 5.0 2.1 + - - +
382C LYS* 3.3 46.1 + - - +
385C ILE* 3.5 15.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 375 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371C ASN* 3.2 18.9 + - + +
372C ILE* 3.1 11.0 + - - +
374C SER* 1.3 79.3 - - - +
376C GLN* 1.3 74.3 + - - +
377C LEU 3.5 0.3 + - - -
378C PRO* 4.0 10.7 - - - +
429C THR* 5.9 1.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 376 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372C ILE* 2.9 22.4 + - + +
373C PHE 4.0 0.7 - - - +
375C ARG* 1.3 85.2 + - - +
377C LEU* 1.3 62.2 + - + +
378C PRO* 3.1 10.0 - - - +
427C ALA* 3.8 10.8 - - + -
428C VAL 3.7 14.6 - - - +
429C THR* 4.9 0.6 - - - +
430C ALA* 3.8 27.1 - - - +
433C GLN* 2.8 22.7 + - - +
314D LYX 3.2 44.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 377 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373C PHE* 2.8 27.5 + - + +
374C SER 3.4 7.7 - - - +
376C GLN* 1.3 76.4 - - + +
378C PRO* 1.3 59.5 - - - +
379C LYS 3.2 2.9 - - - -
380C MET* 3.0 43.3 + - + +
385C ILE* 4.6 1.7 - - + +
425C PHE* 3.8 36.1 - - + -
426C LEU 4.8 3.4 - - - +
427C ALA* 5.5 0.2 - - + -
314D LYX 3.5 59.5 - - + +
----------------------------------------------------------
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