Contacts of the helix formed by residues 5248 - 5259 (chain a) in PDB entry 3A0B
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 ILE5248 (chain a).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5244a GLU* 3.5 27.8 - - - +
5246a TYR* 3.2 36.6 - - + +
5247a ASN* 1.3 74.1 - - - +
5249a VAL* 1.3 68.3 + - + +
5250a ALA 3.0 1.1 - - - -
5251a ALA* 2.9 6.6 + - - +
5252a HIS* 2.8 26.7 + - + +
5265a PHE 5.4 4.3 - - - +
5266a ASN 4.2 13.7 - - - +
5267a ASN 5.6 0.2 - - - -
5268a SER* 3.6 17.3 - - - +
5271a LEU* 5.6 3.1 - - + -
6043a PQ9 4.4 5.8 - - + +
5236d ASN* 4.1 20.6 - - - +
5238d THR* 4.0 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL5249 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5247a ASN* 3.7 3.2 - - - +
5248a ILE* 1.3 82.3 - - + +
5250a ALA* 1.3 58.4 + - - +
5252a HIS* 4.4 9.6 - - + +
5253a GLY* 2.9 27.0 + - - +
5266a ASN* 5.2 2.7 - - - +
5484b SER 5.6 2.0 - - - +
5485b PRO* 4.1 19.7 - - + +
5486b GLU* 4.6 3.3 - - - +
5237d PRO* 2.9 43.5 - - + +
5238d THR* 3.9 10.0 + - + -
5003e GLY* 5.4 6.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA5250 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5222a SER* 3.9 6.5 - - - +
5247a ASN* 2.6 42.7 - - + +
5249a VAL* 1.3 77.7 - - - +
5251a ALA* 1.3 61.8 + - - +
5253a GLY* 4.1 3.2 + - - -
5254a TYR* 4.3 3.6 + - - +
5479b ILE* 5.0 9.4 - - + -
5483b LEU* 6.3 3.1 - - + -
5486b GLU* 5.5 3.1 - - - -
5136d VAL* 4.7 8.6 - - - +
5138d VAL* 4.3 14.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA5251 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5218a LEU* 4.5 12.4 - - + +
5222a SER* 3.7 17.0 + - - +
5246a TYR* 5.2 4.5 - - + -
5247a ASN 3.4 15.2 + - - +
5248a ILE* 2.9 11.4 + - - +
5250a ALA* 1.3 76.1 - - - +
5252a HIS* 1.3 69.3 + - - +
5253a GLY 2.9 0.9 - - - -
5254a TYR* 2.6 26.7 + - - +
5255a PHE 3.8 1.2 + - - -
6043a PQ9 3.6 20.2 - - + -
5138d VAL* 5.6 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS5252 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5248a ILE* 2.8 18.6 + - + +
5249a VAL* 4.3 9.1 - - + +
5251a ALA* 1.3 71.1 - - - +
5253a GLY* 1.3 70.0 + - - +
5254a TYR 2.6 1.9 + - - -
5255a PHE* 3.1 2.2 + - - +
5256a GLY* 2.7 39.6 + - - -
5257a ARG* 5.4 2.7 - - - -
5261a GLN* 3.8 24.5 - - + +
5262a TYR 4.8 1.2 + - - -
5264a SER* 3.3 29.4 + - - -
5265a PHE 2.8 39.0 - - - +
5266a ASN* 3.6 11.5 + - + +
6043a PQ9 3.5 8.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY5253 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5249a VAL* 2.9 21.1 + - - -
5250a ALA 4.3 3.1 - - - -
5251a ALA 2.8 1.2 + - - -
5252a HIS* 1.3 82.0 + - - +
5254a TYR* 1.3 57.5 + - - +
5257a ARG* 3.0 36.2 + - - +
5486b GLU* 4.4 17.7 - - - -
5136d VAL* 4.0 9.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR5254 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5218a LEU* 4.1 15.5 - - + -
5221a SER* 4.1 11.4 - - - -
5250a ALA 4.3 2.1 + - - +
5251a ALA* 2.6 19.4 + - - +
5252a HIS 2.6 0.2 + - - -
5253a GLY* 1.3 68.7 - - - -
5255a PHE* 1.3 54.9 + - - +
5256a GLY 3.2 0.9 - - - -
5257a ARG* 2.6 28.1 + - - +
5258a LEU* 2.7 20.5 + - + -
5129d GLN* 2.6 53.1 + - + +
5132d ILE* 3.4 26.5 - - + -
5133d ALA* 3.8 13.3 - - + +
5136d VAL* 4.5 3.1 - - + +
5138d VAL* 4.0 29.4 - - + -
5139d ARG 4.9 0.9 - - - -
5142d ASN* 2.7 33.3 + - + +
5143d ALA* 4.3 0.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE5255 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5214a MET* 4.7 2.9 - - - -
5218a LEU* 3.9 24.6 - - + +
5251a ALA 3.8 1.2 + - - -
5252a HIS 3.1 1.9 + - - +
5254a TYR* 1.3 75.7 - - - +
5256a GLY* 1.3 62.9 + - - +
5257a ARG 2.8 1.6 - - - -
5258a LEU* 2.5 45.7 + - + +
5259a ILE* 2.8 28.6 + - + +
5263a ALA 4.5 8.5 - - - -
5264a SER* 3.2 17.5 - - - +
6039a PHO 3.4 44.6 - - - -
6043a PQ9 3.5 61.5 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY5256 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5252a HIS* 2.7 30.8 + - - -
5253a GLY 4.5 0.7 - - - -
5255a PHE* 1.3 71.0 - - - +
5257a ARG* 1.3 60.7 + - - +
5259a ILE 2.4 19.4 - - - +
5260a PHE* 3.1 1.9 - - - -
5261a GLN* 3.0 22.6 + - - +
5264a SER* 3.0 23.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG5257 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5252a HIS* 5.4 2.0 - - - -
5253a GLY* 3.0 25.4 + - - +
5254a TYR 2.6 19.3 + - - +
5256a GLY* 1.3 72.7 - - - +
5258a LEU* 1.3 64.8 + - - +
5259a ILE 4.4 1.6 - - - -
5260a PHE 4.7 0.2 + - - -
5261a GLN* 2.8 32.1 + - - +
5486b GLU 3.5 23.1 + - - -
5025d ASP* 2.8 42.7 + - - +
5026d ARG 5.1 2.4 + - - -
5029d PHE* 3.6 34.9 + - + +
5128d ARG* 3.9 0.2 + - - -
5132d ILE* 3.5 25.2 - - + +
5136d VAL* 4.2 10.8 - - + -
5003e GLY 3.8 9.5 - - - +
5004e THR* 3.0 17.1 + - - -
5005e THR* 4.6 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU5258 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5218a LEU* 6.2 0.7 - - + -
5254a TYR* 2.7 11.3 + - + +
5255a PHE* 2.5 36.5 + - + +
5257a ARG* 1.3 69.3 - - - +
5259a ILE* 1.3 63.5 + - + +
6039a PHO 3.3 26.0 - - - +
5125d PHE* 3.9 13.5 - - + -
5128d ARG* 2.3 71.8 + - + +
5129d GLN* 3.5 23.6 - - + -
5132d ILE* 3.4 11.2 - - + +
5142d ASN* 3.4 22.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE5259 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5255a PHE* 2.8 33.7 + - + +
5256a GLY* 2.4 20.2 - - - +
5257a ARG 4.4 0.2 - - - -
5258a LEU* 1.3 83.8 - - + +
5260a PHE* 1.3 84.8 + - + +
5263a ALA* 3.2 29.9 - - + +
5264a SER 4.8 0.2 + - - -
6039a PHO 4.9 3.6 - - - -
6043a PQ9 3.5 59.9 - - + -
5028d VAL* 5.6 2.9 - - + -
5125d PHE* 5.4 7.0 - - + -
5128d ARG* 5.0 3.1 - - - +
----------------------------------------------------------
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