Contacts of the helix formed by residues 420 - 431 (chain B) in PDB entry 2P1N
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 LEU 420 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384B MET* 4.3 8.7 - - + +
385B THR* 3.7 12.3 - - - +
386B ASN* 3.1 42.6 - - - +
389B LEU* 4.6 2.5 - - + -
406B ILE* 3.5 32.5 - - + -
411B ALA 4.1 12.1 - - - +
412B PRO 4.9 1.8 - - - +
413B ASP* 4.0 21.1 - - + +
419B PRO* 1.3 68.2 - - - +
421B ASP* 1.3 68.6 + - - +
423B GLY 3.0 10.6 + - - -
424B PHE* 3.1 24.2 + - + -
440B SER 3.9 10.8 - - - +
441B GLY* 4.3 0.9 - - - -
442B LEU 2.8 9.2 + - - +
443B LEU* 4.0 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 421 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419B PRO* 3.1 11.5 - - + +
420B LEU* 1.3 76.3 - - - +
422B ILE* 1.3 61.8 + - + +
424B PHE* 3.5 0.9 + - - -
425B GLY 2.7 24.4 + - - -
443B LEU* 3.3 10.0 - - - -
444B THR* 2.7 53.7 + - - +
446B LYS* 3.9 8.2 - - + +
447B VAL* 3.4 31.6 - - - +
450B TYR* 3.5 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 422 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386B ASN* 3.7 29.6 - - + +
390B ILE* 4.3 15.0 - - + +
418B GLU* 5.8 3.8 - - + -
419B PRO 5.0 1.1 - - - +
420B LEU 3.1 0.8 + - - -
421B ASP* 1.3 78.6 - - + +
423B GLY* 1.3 60.0 + - - +
425B GLY* 4.1 0.9 - - - +
426B ALA* 2.8 29.6 + - - +
450B TYR* 3.8 24.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 423 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386B ASN* 2.9 28.0 + - - -
389B LEU* 3.4 35.2 - - - +
390B ILE* 4.4 2.9 - - - -
420B LEU 3.0 1.0 + - - -
422B ILE* 1.3 74.8 - - - +
424B PHE* 1.3 62.6 + - - +
426B ALA* 3.1 14.0 + - - +
427B ILE* 3.2 10.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 424 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389B LEU* 4.1 11.9 - - + -
402B PHE* 4.2 15.3 - + - -
404B LEU* 3.0 37.7 - - + -
420B LEU* 3.1 26.8 + - + -
423B GLY* 1.3 72.2 - - - +
425B GLY* 1.3 67.8 + - - +
427B ILE* 3.1 19.6 + - + +
428B VAL* 3.1 15.6 + - - +
437B LEU* 4.4 14.8 - - + +
439B LEU* 3.5 35.2 - - + -
440B SER 3.5 22.4 - - - -
443B LEU* 3.8 14.1 - - + -
447B VAL* 3.5 21.5 - - + -
450B TYR* 5.4 0.2 - - - -
451B ILE* 5.9 1.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 425 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421B ASP 2.7 16.3 + - - -
422B ILE* 3.3 2.2 + - - -
424B PHE* 1.3 68.5 - - - +
426B ALA* 1.3 64.9 + - - +
428B VAL* 2.8 5.1 + - - +
429B GLU* 2.8 28.4 + - - +
450B TYR* 3.3 39.4 - - - -
454B TYR* 5.8 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 426 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390B ILE* 4.0 32.3 - - + -
393B ALA* 3.2 15.8 - - + +
394B ARG* 6.1 0.9 - - - +
422B ILE 2.8 14.0 + - - +
423B GLY 3.1 8.7 + - - +
425B GLY* 1.3 77.8 - - - +
427B ILE* 1.3 61.8 + - - +
429B GLU* 4.4 10.5 - - - +
430B HIS* 2.8 28.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 427 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389B LEU* 3.9 13.2 - - + +
392B ILE* 4.2 13.9 - - + -
393B ALA* 3.6 26.7 - - + +
399B MET* 5.9 1.1 - - + -
402B PHE* 4.0 38.8 - - + -
423B GLY 3.2 13.4 + - - +
424B PHE* 3.1 18.0 + - + +
426B ALA* 1.3 76.7 - - - +
428B VAL* 1.3 61.3 + - + +
431B CYS* 3.0 45.5 + - - +
434B LEU* 3.7 23.1 - - + +
437B LEU* 4.8 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 428 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424B PHE 3.1 10.1 + - - +
425B GLY 2.8 8.8 + - - +
427B ILE* 1.3 81.0 - - + +
429B GLU* 1.3 67.2 + - - +
431B CYS 3.9 10.4 + - - +
432B LYS* 5.0 1.0 - - - +
434B LEU* 4.1 20.0 - - + -
437B LEU* 4.2 18.2 - - + -
450B TYR* 3.5 36.3 - - + +
451B ILE* 4.2 9.0 - - + -
454B TYR* 3.4 22.2 - - + +
455B ALA* 3.7 25.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 429 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425B GLY 2.8 19.2 + - - +
426B ALA* 4.0 8.1 - - - +
428B VAL* 1.3 75.7 - - - +
430B HIS* 1.3 88.3 + - + +
432B LYS* 3.8 16.3 - - - +
454B TYR* 3.5 50.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 430 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390B ILE* 5.5 0.7 - - + -
393B ALA* 4.1 18.6 - - + +
394B ARG* 3.7 47.4 + - + -
397B PRO* 3.6 20.1 - - + +
426B ALA* 2.8 26.7 + - + +
429B GLU* 1.3 114.5 + - + +
431B CYS* 1.3 59.1 + - - +
432B LYS* 3.5 8.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 431 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393B ALA* 4.4 12.8 - - - -
396B ARG* 3.7 20.6 - - - -
397B PRO* 3.7 9.2 - - - +
399B MET* 3.9 26.7 - - + +
427B ILE* 3.0 42.0 + - + +
428B VAL 4.0 7.6 - - - +
429B GLU 3.5 1.4 - - - -
430B HIS* 1.3 77.8 - - - +
432B LYS* 1.3 65.6 + - - +
433B ASP 3.1 2.9 - - - -
434B LEU* 3.0 24.5 + - + +
----------------------------------------------------------
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