Contacts of the helix formed by residues 352 - 365 (chain B) in PDB entry 2NYM
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 ASN 352 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B PRO 5.6 0.2 + - - -
310B PHE* 4.0 21.7 - - + -
311B VAL* 4.4 16.2 - - - +
314B MSE 3.7 24.5 - - - +
348B LEU* 3.2 16.4 + - - +
349B ILE 3.0 5.2 + - - +
350B SER 2.5 6.5 + - - -
351B ASP* 1.3 86.0 - - - +
353B ALA* 1.3 64.7 + - - +
354B ALA* 3.1 7.6 + - - -
355B LYS* 3.3 12.0 + - + +
356B ILE* 3.3 12.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 353 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349B ILE 2.6 15.8 + - - +
350B SER* 2.7 16.4 + - - +
352B ASN* 1.3 70.3 - - - +
354B ALA* 1.3 69.1 + - - +
355B LYS 2.8 1.6 + - - -
356B ILE* 3.0 10.8 + - - -
357B LEU* 3.1 22.5 + - + +
390B MSE 4.1 20.9 - - + -
391B ASN* 4.8 9.9 - - + +
394B LEU* 3.8 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 354 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352B ASN* 3.1 5.1 - - - +
353B ALA* 1.3 78.8 - - - +
355B LYS* 1.3 63.4 + - + +
358B PRO* 3.4 15.9 - - - +
394B LEU* 3.7 25.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 355 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B MSE 4.7 18.2 - - + -
315B GLU* 3.8 35.1 + - + +
352B ASN* 3.3 6.5 + - + +
353B ALA 2.8 2.2 + - - -
354B ALA* 1.3 83.2 - - + +
356B ILE* 1.3 61.0 + - + +
358B PRO* 3.0 20.1 - - - +
359B ILE* 3.6 14.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 356 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B PHE* 3.9 24.0 - - + -
314B MSE 3.8 21.5 - - + +
318B PHE* 4.0 29.2 - - + -
349B ILE* 3.4 51.8 - - + +
352B ASN* 3.3 11.7 + - + +
353B ALA 3.0 2.6 + - - +
355B LYS* 1.3 71.0 - - - +
357B LEU* 1.3 58.7 + - - +
358B PRO* 3.1 3.6 - - - -
359B ILE* 2.6 43.8 + - + +
360B MSE 3.2 12.7 + - + -
387B PHE* 4.5 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 357 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353B ALA* 3.1 17.7 + - + +
354B ALA 5.0 0.2 - - - +
356B ILE* 1.3 80.8 - - - +
358B PRO* 1.3 62.9 - - + +
360B MSE 3.4 1.5 + - - +
361B PHE* 3.0 55.3 + - + -
387B PHE* 3.0 45.3 - - + +
390B MSE 3.3 22.0 - - + -
391B ASN* 5.8 2.0 - - + +
394B LEU* 5.0 6.1 - - + -
395B PHE* 4.8 11.0 - - + +
398B CYS* 4.1 15.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 358 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354B ALA 3.4 18.2 - - - +
355B LYS* 3.0 18.8 - - - +
356B ILE 3.1 4.0 - - - -
357B LEU* 1.3 95.6 - - + +
359B ILE* 1.3 59.6 + - + +
360B MSE 3.2 0.2 - - - -
361B PHE* 3.8 6.2 - - + +
362B PRO* 3.2 22.9 - - - +
398B CYS* 4.7 15.5 - - + -
401B GLN* 6.0 2.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 359 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315B GLU* 4.2 39.0 - - + +
318B PHE* 3.9 12.6 - - + +
319B ARG* 3.7 43.5 - - + +
322B ALA* 3.8 13.9 - - + +
355B LYS 3.6 22.0 - - - +
356B ILE* 2.6 19.1 + - + +
358B PRO* 1.3 73.9 - - + +
360B MSE 1.3 57.1 + - + +
361B PHE 3.5 0.2 - - - -
362B PRO* 4.1 8.2 - - - +
363B SER* 4.0 2.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 360 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B PHE* 3.0 46.9 - - + +
321B LEU* 3.3 29.2 - - + +
322B ALA* 3.9 20.2 - - - -
325B VAL* 4.9 3.1 - - - -
340B TRP* 3.4 32.8 - - + -
356B ILE* 3.2 13.8 + - + +
357B LEU 3.9 6.5 - - - +
359B ILE* 1.3 81.2 - - - +
361B PHE* 1.3 60.7 + - - +
363B SER* 2.8 18.4 + - - -
364B LEU* 3.0 31.2 + - + +
387B PHE* 4.3 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 361 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357B LEU* 3.0 46.9 + - + +
358B PRO* 4.1 5.8 - - + +
360B MSE 1.3 72.8 - - - +
362B PRO* 1.3 64.5 - - + +
363B SER 2.5 18.0 + - - -
364B LEU* 2.7 14.0 + - + -
365B TYR* 2.8 52.6 + + + +
384B LEU* 4.7 7.6 - - + -
387B PHE* 5.1 0.9 - + - -
395B PHE* 3.7 39.7 - + - -
398B CYS* 4.1 16.2 - - + +
399B THR* 3.9 24.0 - - - -
402B PHE* 4.7 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 362 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358B PRO 3.2 16.8 - - - +
359B ILE 4.1 9.9 - - - +
360B MSE 3.8 0.4 - - - -
361B PHE* 1.3 94.2 - - + +
363B SER* 1.3 58.3 + - - +
365B TYR* 5.2 0.4 - - + -
366B ARG* 3.0 27.8 + - - +
402B PHE* 4.7 27.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 363 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322B ALA* 3.5 21.3 + - - +
325B VAL* 4.3 10.6 - - - +
326B SER* 3.0 31.0 + - - -
359B ILE 4.0 5.5 + - - -
360B MSE 2.8 25.6 + - - -
361B PHE 2.5 8.3 + - - -
362B PRO* 1.3 76.0 - - - +
364B LEU* 1.3 62.7 + - - +
366B ARG* 3.0 19.8 - - - +
380B ILE* 4.5 4.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 364 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B VAL* 3.8 27.8 - - + -
337B LEU* 5.1 2.0 - - + -
340B TRP* 4.1 28.9 - - + +
360B MSE 3.0 36.3 + - + +
361B PHE* 2.7 9.0 + - + +
363B SER* 1.3 71.8 - - - +
365B TYR* 1.3 58.9 + - - +
366B ARG 2.9 8.1 + - - +
368B SER* 3.8 7.6 + - - -
380B ILE* 3.1 29.9 - - + +
383B ALA* 4.6 13.9 - - + -
384B LEU* 3.6 28.8 - - + +
387B PHE* 4.4 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 365 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361B PHE* 2.8 44.8 + + + +
362B PRO 4.3 0.4 - - - -
364B LEU* 1.3 74.9 - - - +
366B ARG* 1.3 70.9 + - - +
367B ASN* 4.2 4.5 - - - +
384B LEU* 4.1 21.1 - - + -
395B PHE* 5.5 4.0 - + - -
399B THR* 4.3 17.0 - - + +
402B PHE* 3.2 38.1 - + + -
403B LYS* 3.5 26.8 - - + +
----------------------------------------------------------
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