Contacts of the helix formed by residues 415 - 431 (chain O) in PDB entry 2I2X
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 SER 415 (chain O).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414O LEU* 1.3 73.2 - - - +
416O ARG* 1.3 59.9 + - - +
417O PHE* 3.5 6.1 + - - +
418O GLU* 2.9 40.6 + - - +
419O THR* 2.9 31.3 + - - -
17P ASN* 4.1 14.5 + - - -
18P VAL* 3.8 18.5 - - - +
21P GLU* 3.5 18.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 416 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414O LEU 3.9 0.2 + - - -
415O SER* 1.3 72.3 - - - +
417O PHE* 1.3 55.3 + - - +
419O THR* 3.4 7.1 + - - -
420O LYS* 3.0 30.7 + - - +
18P VAL 5.7 1.8 + - - -
21P GLU* 2.8 42.7 + - - +
22P LYS 2.9 30.9 + - - -
23P ALA* 3.6 15.2 + - - +
24P LEU 5.7 0.6 + - - -
25P THR* 6.2 3.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 417 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179O ASN* 6.3 1.3 - - - -
239O ALA* 4.6 13.0 - - + -
415O SER* 3.2 4.2 - - - +
416O ARG* 1.3 76.6 - - - +
418O GLU* 1.3 58.0 + - + +
420O LYS* 3.4 6.6 + - + +
421O ALA* 3.1 28.7 + - + +
21P GLU* 2.9 19.0 + - - +
26P PRO* 4.3 18.8 - - + -
92P VAL 3.4 25.6 - - - -
93P ILE* 4.2 3.4 - - + -
94P PHE* 3.4 49.6 - + + -
97P ASN* 3.6 26.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 418 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233O LEU 5.5 1.0 - - - +
239O ALA* 5.0 4.7 - - + -
240O HIS* 3.9 28.2 + - - +
241O THR* 2.9 44.6 + - + +
365O PRO* 5.0 0.7 - - - -
414O LEU* 3.5 9.7 - - + +
415O SER* 2.9 38.7 + - - +
417O PHE* 1.3 75.3 - - + +
419O THR* 1.3 66.3 + - - +
421O ALA* 3.6 1.0 + - - -
422O LEU* 3.3 9.0 + - - +
15P ARG* 2.9 37.9 + - - -
17P ASN* 3.7 7.8 - - - +
94P PHE* 6.2 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 419 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408O ALA* 5.5 3.0 - - + +
414O LEU* 3.4 26.0 + - + +
415O SER 2.9 19.5 + - - -
416O ARG* 3.6 8.5 - - - +
418O GLU* 1.3 76.4 - - - +
420O LYS* 1.3 62.3 + - - +
422O LEU* 3.6 7.5 + - + +
423O ALA* 3.3 20.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 420 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416O ARG 3.0 18.1 + - - +
417O PHE* 3.7 7.6 - - + +
418O GLU 3.2 0.2 - - - -
419O THR* 1.3 72.4 - - - +
421O ALA* 1.3 64.3 + - - +
422O LEU 3.1 1.9 + - - -
423O ALA* 3.3 11.7 + - + +
424O ASP* 3.1 52.4 + - - +
27P GLU* 5.2 10.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 421 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179O ASN* 5.8 1.8 - - - +
181O ILE* 5.7 0.2 - - - +
239O ALA* 3.8 18.6 - - + -
241O THR* 3.7 16.6 - - - +
242O ILE* 3.9 18.9 - - + +
417O PHE* 3.1 18.8 + - + +
420O LYS* 1.3 75.5 - - - +
422O LEU* 1.3 55.9 + - - +
424O ASP* 3.7 10.2 - - - +
425O ALA* 3.0 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 422 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241O THR* 3.8 16.0 + - + +
245O ILE* 4.1 11.9 - - + -
401O CYS* 3.7 35.7 - - - -
404O ILE* 3.8 33.9 - - + -
405O GLU* 3.8 30.5 - - + +
408O ALA* 6.2 0.2 - - + -
414O LEU* 4.6 9.6 - - + -
418O GLU 3.3 14.5 + - - +
419O THR* 3.6 6.7 - - + +
420O LYS 3.1 0.6 - - - -
421O ALA* 1.3 74.7 - - - +
423O ALA* 1.3 61.5 + - - +
424O ASP 3.1 1.6 - - - -
425O ALA* 3.0 5.4 + - - +
426O LYS* 2.8 31.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 423 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405O GLU* 4.9 8.0 + - - +
419O THR* 3.3 10.2 + - + +
420O LYS* 3.3 15.7 + - + +
422O LEU* 1.3 78.1 - - - +
424O ASP* 1.3 58.9 + - - +
426O LYS* 3.7 6.2 - - - +
427O ALA* 2.9 31.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 424 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181O ILE* 5.5 0.4 - - - -
420O LYS* 3.1 51.6 + - - +
421O ALA* 3.7 8.4 - - - +
423O ALA* 1.3 75.0 - - - +
425O ALA* 1.3 60.8 + - - +
427O ALA* 3.6 5.7 + - - +
428O ALA* 3.0 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 425 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181O ILE* 3.9 31.1 - - + +
242O ILE* 5.0 2.0 - - + -
245O ILE* 3.5 28.7 - - + -
421O ALA 3.0 19.2 + - - +
422O LEU* 3.0 4.5 + - - +
424O ASP* 1.3 74.3 - - - +
426O LYS* 1.3 63.7 + - - +
428O ALA* 3.2 4.2 + - - +
429O LEU* 3.0 29.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 426 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398O ILE* 4.9 4.2 - - + +
401O CYS* 3.7 29.7 - - + -
402O ASN* 3.3 20.6 + - - +
405O GLU* 3.2 34.9 + - - +
422O LEU* 2.8 19.7 + - + +
423O ALA* 3.7 6.3 - - - +
425O ALA* 1.3 71.8 - - - +
427O ALA* 1.3 59.5 + - - +
429O LEU* 3.1 7.2 + - - +
430O GLU* 2.8 66.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 427 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423O ALA 2.9 21.4 + - - +
424O ASP* 3.8 6.3 - - - +
426O LYS* 1.3 71.6 - - - +
428O ALA* 1.3 63.9 + - - +
430O GLU* 3.2 8.6 + - - +
431O ALA* 3.1 24.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 428 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181O ILE* 4.6 6.7 - - + -
182O PRO* 4.4 23.3 - - + +
424O ASP 3.0 18.9 + - - +
425O ALA* 3.2 7.8 + - - +
427O ALA* 1.3 75.1 - - - +
429O LEU* 1.3 60.8 + - - +
431O ALA* 3.5 12.2 + - - +
432O LEU* 3.4 20.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 429 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181O ILE* 4.0 28.0 - - + +
182O PRO* 6.2 0.2 - - + -
185O LEU* 4.1 19.5 - - + -
245O ILE* 4.5 6.1 - - + -
249O ILE* 5.3 0.7 - - + -
394O LYS* 4.1 10.6 + - + +
397O ALA* 3.8 39.7 - - + -
398O ILE* 3.9 22.8 - - + +
401O CYS* 4.5 8.5 - - - -
425O ALA* 3.0 23.5 + - + +
426O LYS 3.6 4.5 - - - +
428O ALA* 1.3 73.6 - - - +
430O GLU* 1.3 63.9 + - - +
431O ALA 3.1 2.5 + - - -
432O LEU* 3.3 36.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 430 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398O ILE* 3.7 26.5 - - + +
426O LYS* 2.8 66.1 + - + +
427O ALA* 3.2 7.5 + - - +
429O LEU* 1.3 72.4 - - - +
431O ALA* 1.3 58.8 - - - +
432O LEU 3.3 4.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 431 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427O ALA 3.1 15.4 + - - +
428O ALA* 3.7 9.4 - - - +
429O LEU 3.1 0.8 - - - -
430O GLU* 1.3 74.0 - - - +
432O LEU* 1.3 66.6 + - + +
433O PRO* 4.5 1.0 - - - +
----------------------------------------------------------
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