Contacts of the helix formed by residues 435 - 451 (chain I) 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 ASP 435 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390I TYR* 4.2 2.3 - - - -
433I PRO* 3.2 4.8 - - + +
434I ASP* 1.3 79.0 - - - +
436I MET* 1.3 67.0 + - - +
437I ASP* 3.7 18.5 + - - +
438I LYS* 2.9 39.1 + - + +
439I PHE* 3.2 19.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 436 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194I ILE* 5.4 1.6 - - + -
388I ASN* 4.0 22.4 - - - +
389I ILE* 3.8 33.2 - - + -
390I TYR* 3.6 35.6 - - + -
434I ASP 3.7 4.2 + - - -
435I ASP* 1.3 73.4 + - - +
437I ASP* 1.3 61.4 + - - +
439I PHE* 2.9 4.7 + - - +
440I MET* 2.7 69.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 437 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435I ASP* 3.4 16.6 + - - +
436I MET* 1.3 82.2 - - - +
438I LYS* 1.3 60.1 + - - +
440I MET* 3.9 6.5 - - - +
441I ASP* 2.8 37.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 438 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433I PRO* 4.4 19.3 - - + -
435I ASP* 2.9 27.3 + - + +
436I MET 3.1 0.2 - - - -
437I ASP* 1.3 75.6 - - - +
439I PHE* 1.3 62.9 + - - +
441I ASP* 3.4 5.1 + - - +
442I ASP* 3.1 57.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 439 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182I PRO* 3.6 22.7 - - + -
185I LEU* 4.1 6.1 - - + -
186I TYR* 3.9 22.7 - + + -
190I CYS* 4.1 6.5 - - - -
390I TYR* 3.1 53.6 - + + +
432I LEU* 3.7 36.3 - - + -
433I PRO* 4.2 9.3 - - + +
435I ASP 3.2 4.6 + - - +
436I MET 2.9 7.0 + - - +
438I LYS* 1.3 78.2 - - - +
440I MET* 1.3 67.5 + - - +
442I ASP* 4.0 4.9 - - + +
443I CYS* 3.1 50.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 440 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186I TYR* 3.8 22.6 + - + -
190I CYS* 3.6 33.9 - - + -
191I LEU* 5.1 0.4 - - + -
194I ILE* 4.0 16.4 - - + -
436I MET* 2.7 53.1 + - + +
437I ASP* 3.9 7.9 - - - +
439I PHE* 1.3 75.4 - - + +
441I ASP* 1.3 60.5 + - - +
443I CYS* 4.0 1.2 - - - +
444I LEU* 3.0 29.3 + - - +
461I PHE* 3.8 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 441 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437I ASP* 2.8 31.0 + - - +
438I LYS* 3.7 5.5 - - - +
439I PHE 3.2 0.2 - - - -
440I MET* 1.3 78.4 - - - +
442I ASP* 1.3 68.4 + - - +
443I CYS 3.3 0.2 - - - -
444I LEU* 3.4 10.8 + - - +
445I THR* 3.0 31.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 442 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433I PRO* 5.3 3.3 - - - +
438I LYS* 3.1 47.7 + - - +
439I PHE* 4.0 6.3 - - + +
441I ASP* 1.3 77.2 - - - +
443I CYS* 1.3 54.6 + - - +
445I THR* 3.4 8.2 + - - -
446I LYS* 2.8 37.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 443 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182I PRO* 4.7 3.8 - - - -
186I TYR* 3.4 37.2 - - + -
439I PHE* 3.1 54.8 + - - +
442I ASP* 1.3 78.7 - - - +
444I LEU* 1.3 65.5 + - - +
446I LYS* 4.2 4.7 - - - -
447I TYR* 2.8 43.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 444 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186I TYR* 3.9 11.4 + - - +
440I MET 3.0 20.8 + - - +
441I ASP* 3.7 13.9 - - - +
442I ASP 3.4 0.2 - - - -
443I CYS* 1.3 74.2 - - - +
445I THR* 1.3 62.6 + - + +
447I TYR 4.0 0.2 - - - -
448I LYS* 2.9 56.4 + - + +
454I PHE* 4.0 11.7 - - + -
456I PRO* 3.8 24.5 - - + -
461I PHE* 4.7 22.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 445 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441I ASP* 3.0 19.0 + - + +
442I ASP* 3.6 6.3 + - - -
443I CYS 3.2 0.2 - - - -
444I LEU* 1.3 78.5 - - + +
446I LYS* 1.3 69.2 + - - +
448I LYS* 3.5 10.6 + - + +
449I SER* 3.1 23.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 446 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180I ASP* 3.9 8.3 + - - -
182I PRO* 6.2 2.0 - - + -
442I ASP 2.8 19.7 + - - +
443I CYS* 3.8 6.1 - - - +
445I THR* 1.3 77.7 + - - +
447I TYR* 1.3 96.9 + - + +
449I SER* 3.2 6.4 + - - -
450I GLU* 2.9 63.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 447 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171I VAL* 4.0 20.6 - - + -
174I TYR* 4.2 15.3 - + - -
175I ALA* 5.5 0.2 - - + -
180I ASP* 2.4 40.5 + - - -
182I PRO* 4.1 2.5 - - + +
183I GLY* 3.2 20.0 + - - -
186I TYR* 3.8 18.2 - + + -
443I CYS* 2.8 45.9 + - - +
446I LYS* 1.3 99.7 - - + +
448I LYS* 1.3 65.2 + - - +
449I SER 3.1 1.1 - - - -
450I GLU* 3.7 4.0 - - + +
451I VAL* 3.0 44.8 + - + +
454I PHE* 3.7 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 448 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444I LEU* 2.9 47.8 + - + +
445I THR* 3.5 11.0 - - + +
447I TYR* 1.3 78.6 - - - +
449I SER* 1.3 63.6 + - - +
451I VAL 3.9 9.7 - - - +
452I LYS* 4.9 6.6 - - - +
454I PHE* 3.8 9.5 - - + +
456I PRO* 4.1 27.5 - - + +
461I PHE 6.0 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 449 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445I THR 3.1 14.2 + - - -
446I LYS* 3.5 9.4 + - - -
448I LYS* 1.3 81.2 - - - +
450I GLU* 1.3 68.0 + - - +
451I VAL 3.5 0.3 + - - -
452I LYS* 4.5 16.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 450 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174I TYR* 2.9 48.7 + - + +
180I ASP* 4.9 1.0 - - - +
446I LYS* 2.9 62.7 + - - +
447I TYR* 3.6 2.4 + - + -
449I SER* 1.3 79.3 - - - +
451I VAL* 1.3 63.7 + - + +
452I LYS* 4.1 2.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 451 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170I GLU* 4.3 17.9 - - + +
171I VAL* 4.9 4.7 - - + -
174I TYR* 3.6 38.1 - - + -
447I TYR* 3.0 36.2 + - + +
448I LYS 3.9 6.8 - - - +
449I SER 3.4 0.6 - - - -
450I GLU* 1.3 81.6 - - - +
452I LYS* 1.3 63.9 + - - +
453I VAL* 3.8 23.3 - - + -
454I PHE* 3.1 24.1 + - + +
----------------------------------------------------------
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