Contacts of the helix formed by residues 5426 - 5439 (chain E) in PDB entry 2H7C
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 PHE5426 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5E COA 4.8 6.3 - - + -
5221E SER* 4.7 4.0 - - - -
5247E SER* 3.2 36.1 - - - -
5248E GLY* 4.0 5.4 - - - -
5252E THR* 4.4 12.6 - - + -
5255E LEU* 6.4 0.4 - - + -
5350E ILE* 4.3 6.7 - - + -
5354E GLU* 3.4 39.7 - - + +
5355E PHE* 5.1 1.3 - + - -
5359E ILE* 3.7 32.5 - - + -
5422E ALA* 2.9 15.5 + - - +
5425E MET* 1.3 106.6 - - + +
5427E GLY* 1.3 63.7 + - - +
5429E PRO* 3.6 4.0 - - - -
5430E SER* 2.7 34.4 + - - +
5468E HIS* 3.7 10.8 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY5427 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5350E ILE* 4.1 23.2 - - - +
5354E GLU* 5.6 0.4 - - - +
5422E ALA 3.1 10.1 + - - -
5423E ASP* 3.7 9.9 - - - -
5426E PHE* 1.3 80.2 - - - +
5428E VAL* 1.3 63.3 + - - +
5430E SER* 3.7 1.9 - - - -
5431E VAL* 3.2 24.9 + - - +
5540E LYS* 4.4 12.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL5428 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5423E ASP* 2.8 22.9 + - + +
5424E VAL* 5.0 2.0 - - - -
5427E GLY* 1.3 68.3 - - - -
5429E PRO* 1.3 71.7 - - + +
5431E VAL* 3.2 2.6 + - - +
5432E ILE* 2.9 51.1 + - + +
5540E LYS* 5.4 1.1 - - + -
5543E GLU* 4.0 20.4 - - + +
5544E VAL* 4.1 21.8 - - + +
5547E TRP* 3.6 39.9 - - + -
5548E THR* 5.1 0.7 - - - +
5551E PHE* 6.4 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO5429 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5249E VAL* 3.7 9.4 - - + -
5251E LEU* 3.6 43.2 - - + +
5423E ASP 3.4 9.4 - - - +
5424E VAL 3.2 19.5 - - - +
5425E MET 3.5 13.5 - - - +
5426E PHE 3.4 9.6 - - - +
5428E VAL* 1.3 95.6 - - + +
5430E SER* 1.3 55.9 + - - +
5432E ILE* 3.4 3.8 + - + +
5433E VAL* 3.0 33.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER5430 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5248E GLY* 4.7 5.7 + - - -
5249E VAL* 3.8 18.3 - - - +
5348E VAL* 3.7 24.6 - - - +
5349E GLY 4.5 1.6 + - - -
5350E ILE* 3.4 21.7 - - - +
5426E PHE* 2.7 25.0 + - - -
5427E GLY 3.7 2.7 - - - -
5429E PRO* 1.3 74.7 - - - +
5431E VAL* 1.3 59.9 + - - +
5433E VAL* 3.3 2.9 + - - +
5434E ALA* 2.9 29.1 + - - +
5446E MET* 3.9 5.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL5431 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5427E GLY 3.2 16.6 + - - +
5428E VAL 3.2 3.1 + - - +
5430E SER* 1.3 73.9 - - - +
5432E ILE* 1.3 67.6 + - - +
5434E ALA* 3.2 1.7 + - - +
5435E ARG* 2.9 50.1 + - - +
5446E MET* 3.9 21.3 - - + -
5520E TYR* 3.6 11.2 - - - +
5539E LEU* 3.5 30.7 - - + +
5540E LYS* 3.9 10.5 - - + -
5544E VAL* 3.8 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE5432 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5251E LEU* 3.6 21.5 - - + -
5336E GLN* 4.2 1.3 - - - +
5428E VAL* 2.9 39.3 + - + +
5429E PRO* 3.7 5.2 - - + +
5431E VAL* 1.3 75.3 - - - +
5433E VAL* 1.3 59.2 + - - +
5435E ARG* 3.5 8.7 + - - +
5436E ASN* 2.7 47.9 + - - +
5544E VAL* 4.0 16.6 - - + -
5548E THR* 4.2 16.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL5433 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5228E SER* 4.6 7.4 - - - +
5249E VAL* 3.8 26.7 - - + -
5250E ALA* 4.9 1.3 - - + +
5251E LEU* 3.8 17.9 - - + +
5336E GLN* 3.3 21.7 - - - +
5346E TYR* 3.9 28.9 - - + +
5348E VAL* 4.6 2.5 - - + -
5429E PRO 3.0 21.6 + - - +
5430E SER 3.6 5.2 - - - +
5432E ILE* 1.3 73.6 - - - +
5434E ALA* 1.3 59.2 + - - +
5436E ASN* 3.3 2.6 + - - +
5437E HIS* 2.9 27.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA5434 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5348E VAL* 4.5 8.5 - - + +
5430E SER 2.9 13.1 + - - +
5431E VAL 3.2 2.7 + - - +
5433E VAL* 1.3 78.3 - - - +
5435E ARG* 1.3 56.3 + - - +
5437E HIS* 3.2 4.7 + - - +
5438E ARG* 2.8 30.8 + - - +
5444E THR* 3.6 13.1 - - + +
5446E MET* 3.4 40.8 - - + -
5520E TYR* 3.8 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG5435 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5431E VAL* 2.9 33.9 + - - +
5432E ILE* 3.8 8.5 - - - +
5434E ALA* 1.3 75.2 - - - +
5436E ASN* 1.3 60.5 + - - +
5438E ARG* 3.3 23.1 + - - +
5439E ASP* 2.9 37.0 + - - +
5520E TYR* 3.4 21.6 + - + +
5524E GLU* 3.0 34.8 + - - -
5541E ASP* 3.1 33.7 + - - +
5544E VAL* 3.5 25.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN5436 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5336E GLN* 3.3 43.9 - - + +
5337E ALA* 4.9 1.2 + - - -
5339E ARG* 2.6 47.3 + - - +
5341E PHE* 4.4 3.4 - - + -
5432E ILE* 2.7 37.9 + - - +
5433E VAL 3.6 3.8 - - - +
5435E ARG* 1.3 74.3 - - - +
5437E HIS* 1.3 66.7 + - - +
5439E ASP* 3.4 1.1 + - - +
5440E ALA* 3.1 13.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS5437 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5231E VAL* 4.6 8.2 - - + +
5341E PHE* 3.6 31.1 - + + -
5343E THR* 4.8 1.1 - - - -
5344E VAL* 2.7 35.7 + - + -
5346E TYR* 3.2 40.8 - + + +
5433E VAL* 2.9 17.2 + - + +
5434E ALA* 3.5 7.2 - - - +
5436E ASN* 1.3 76.2 - - - +
5438E ARG* 1.3 62.7 + - - +
5440E ALA* 2.9 18.5 + - - +
5441E GLY 3.5 3.1 + - - -
5442E ALA* 3.2 23.2 + - + +
5443E PRO 3.6 4.9 + - - -
5444E THR* 3.0 22.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG5438 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5434E ALA 2.8 17.5 + - - +
5435E ARG* 3.4 25.6 - - - +
5437E HIS* 1.3 78.6 - - - +
5439E ASP* 1.3 87.5 + - - +
5441E GLY* 2.9 22.3 + - - -
5442E ALA 4.1 4.1 - - - +
5444E THR* 3.3 11.6 + - - +
5519E GLU* 5.2 2.5 - - - +
5520E TYR* 3.2 34.1 - - + +
5521E ASN* 3.0 33.2 + - + +
5522E GLN* 3.4 22.7 + - - +
5524E GLU* 3.5 24.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP5439 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5339E ARG* 3.7 28.7 + - - +
5435E ARG* 2.9 22.5 + - - +
5436E ASN* 3.7 1.7 - - - +
5437E HIS 3.3 0.2 - - - -
5438E ARG* 1.3 105.7 + - - +
5440E ALA* 1.3 57.5 + - - +
5441E GLY 3.2 2.2 + - - -
5522E GLN* 3.5 12.0 + - - -
----------------------------------------------------------
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