Contacts of the helix formed by residues 5016 - 5031 (chain m) 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 LEU5016 (chain m).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13M LEU* 3.7 34.3 - - + -
16M LEU* 6.3 1.6 - - + -
17M VAL* 5.9 3.4 - - + -
5012m ALA* 3.1 22.0 - - + +
5013m LEU* 2.4 25.8 + - + +
5014m PHE 3.5 0.2 - - - -
5015m VAL* 1.3 79.5 - - + +
5017m VAL* 1.3 57.8 + - - +
5018m PRO* 3.3 1.1 - - - -
5019m SER* 3.1 3.1 + - - -
5020m VAL* 2.4 42.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL5017 (chain m).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16M LEU* 5.9 3.8 - - + -
6021b CLA 4.5 8.1 - - + -
6022b CLA 6.2 6.5 - - + -
6061d MGE 4.2 26.0 - - + +
5013m LEU* 2.9 33.0 + - + +
5014m PHE* 5.2 1.1 - - - -
5016m LEU* 1.3 70.6 - - - +
5018m PRO* 1.3 72.1 - - + +
5020m VAL* 2.8 27.3 - - - +
5021m PHE* 3.1 8.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO5018 (chain m).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6021b CLA 3.6 12.3 - - + -
6060b MGE 4.6 2.0 - - + -
6061d MGE 3.3 33.3 - - + +
5024l ILE* 3.0 25.1 - - + +
5014m PHE* 2.8 36.6 - - + +
5015m VAL* 4.2 1.3 - - - +
5016m LEU 3.4 1.1 - - - -
5017m VAL* 1.3 101.1 - - + +
5019m SER* 1.3 68.3 + - - +
5021m PHE* 3.0 18.9 - - - +
5022m LEU* 3.7 7.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER5019 (chain m).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5021l LEU* 3.4 25.5 - - - +
5024l ILE* 2.8 22.5 - - - +
5015m VAL* 3.0 27.7 + - - -
5016m LEU* 3.1 3.5 + - - -
5018m PRO* 1.3 75.2 - - - +
5020m VAL* 1.3 68.7 + - - +
5022m LEU* 2.9 19.1 + - - +
5023m ILE* 3.4 17.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL5020 (chain m).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20M VAL* 2.9 39.3 - - + -
24M ILE* 5.0 2.9 - - + -
5016m LEU* 2.4 30.4 + - + +
5017m VAL* 2.8 33.4 - - - +
5019m SER* 1.3 73.1 - - - +
5021m PHE* 1.3 68.3 + - - +
5023m ILE* 2.7 29.2 + - + +
5024m ILE* 2.9 23.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE5021 (chain m).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5002b TRP* 4.0 3.6 - + + -
6019b CLA 3.7 26.9 - - + -
6022b CLA 3.2 35.9 - - + -
6061d MGE 3.3 47.3 - - + -
5017m VAL 3.1 8.0 + - - +
5018m PRO* 3.0 13.9 - - + +
5020m VAL* 1.3 84.0 - - - +
5022m LEU* 1.3 76.0 + - + +
5024m ILE* 3.3 11.4 - - + +
5025m LEU* 3.2 55.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU5022 (chain m).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6061d MGE 3.6 21.1 - - + +
5012l LEU* 5.6 9.4 - - + -
5017l LEU* 3.8 27.0 - - + +
5020l GLY* 3.8 20.4 - - - +
5021l LEU* 3.5 28.7 - - + -
5024l ILE* 4.8 4.5 - - + -
5018m PRO 3.7 7.0 - - - +
5019m SER 2.9 9.3 + - - +
5020m VAL 2.8 0.4 + - - -
5021m PHE* 1.3 109.6 - - + +
5023m ILE* 1.3 55.9 + - - +
5024m ILE 2.7 5.8 - - - -
5025m LEU* 4.4 4.5 - - + +
5026m TYR* 2.8 36.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE5023 (chain m).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1022B CLA 4.4 43.5 - - + -
24M ILE* 3.7 21.8 - - + +
5017l LEU* 5.3 6.3 - - + -
5021l LEU* 4.8 11.9 - - + -
5019m SER* 3.8 24.0 - - - +
5020m VAL* 2.7 21.3 + - + +
5022m LEU* 1.3 71.1 - - - +
5024m ILE* 1.3 57.1 + - - +
5026m TYR* 4.7 5.2 - - + -
5027m VAL* 3.4 26.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE5024 (chain m).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20M VAL* 4.2 5.4 - - + -
23M ILE* 3.9 23.3 - - + +
24M ILE* 4.3 14.5 - - + +
27M VAL* 3.9 29.5 - - + +
6022b CLA 6.0 9.0 - - + -
5020m VAL* 2.9 35.6 + - + +
5021m PHE* 3.3 14.8 - - + +
5022m LEU 2.7 1.8 - - - -
5023m ILE* 1.3 81.0 - - - +
5025m LEU* 1.3 74.7 + - + +
5026m TYR 3.1 1.2 + - - -
5027m VAL* 3.6 3.7 + - - +
5028m GLN* 3.3 21.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU5025 (chain m).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27M VAL* 5.7 1.8 - - + -
36M SER* 6.1 0.2 - - - +
5002b TRP* 3.9 15.7 - - + -
6022b CLA 3.4 28.5 - - + -
5010l VAL* 4.0 20.4 - - + -
5011l GLU 5.0 1.1 - - - +
5012l LEU* 3.7 24.7 - - + +
5021m PHE* 3.2 45.9 + - + +
5022m LEU* 4.6 3.1 - - + +
5024m ILE* 1.3 88.0 - - + +
5026m TYR* 1.3 58.0 + - - +
5028m GLN* 2.6 38.2 + - + +
5029m THR* 3.3 2.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR5026 (chain m).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5012l LEU* 3.5 18.0 - - + +
5013l ASN 4.1 0.4 - - - -
5014l ARG* 3.3 63.4 + - + +
5017l LEU* 3.5 24.7 - - + -
5018l TYR* 6.4 0.4 - + - -
5022m LEU 2.8 20.1 + - - +
5023m ILE* 4.7 2.7 - - + -
5025m LEU* 1.3 77.5 - - - +
5027m VAL* 1.3 74.5 + - + +
5029m THR* 2.5 37.2 + - - -
5030m GLU* 2.9 41.3 + - + +
5036m SER* 6.1 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL5027 (chain m).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24M ILE* 4.0 19.7 - - + +
25M LEU* 5.6 3.1 - - + -
28M GLN* 3.5 21.5 - - + -
5023m ILE* 3.4 29.4 - - + +
5024m ILE 3.6 6.4 + - - +
5026m TYR* 1.3 97.6 - - + +
5028m GLN* 1.3 63.1 + - - +
5029m THR 3.0 1.2 + - - -
5030m GLU* 3.3 13.4 + - - +
5031m SER* 3.4 11.6 + - - -
5036m SER* 3.8 18.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN5028 (chain m).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27M VAL* 3.2 26.9 - - + -
28M GLN* 3.2 14.3 - - - +
31M SER* 2.7 55.9 + - - +
35M SER 3.8 1.4 - - - +
5010l VAL* 2.9 39.8 + - + +
5012l LEU* 4.8 0.8 - - - +
5024m ILE 3.3 8.3 + - - +
5025m LEU* 2.6 26.4 + - + +
5027m VAL* 1.3 79.2 - - - +
5029m THR* 1.3 101.2 + - - +
5031m SER* 3.7 0.9 + - - -
5032m GLN* 3.7 8.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR5029 (chain m).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5010l VAL 4.2 1.7 + - - -
5012l LEU 2.6 34.8 + - - +
5013l ASN* 5.0 2.9 - - - -
5025m LEU 3.3 1.9 + - - -
5026m TYR* 2.5 23.7 + - + -
5028m GLN* 1.3 94.7 + - - +
5030m GLU* 1.3 68.4 + - - +
5031m SER 2.9 4.3 - - - -
5032m GLN* 2.6 45.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU5030 (chain m).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5014l ARG* 4.9 8.8 + - - +
5026m TYR* 2.9 44.0 + - + +
5027m VAL* 3.3 5.8 + - - +
5029m THR* 1.3 93.6 - - - +
5031m SER* 1.3 58.0 + - - +
5032m GLN 3.1 1.6 + - - -
5033m GLN* 3.5 10.2 + - - +
5035m SER* 3.3 24.3 + - - -
5036m SER* 4.1 16.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER5031 (chain m).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28M GLN* 2.4 57.5 + - - +
31M SER 3.2 8.4 - - - +
32M GLN* 2.9 28.7 + - - -
5027m VAL 3.4 1.7 + - - -
5028m GLN 3.8 4.3 - - - -
5029m THR 2.9 0.8 - - - -
5030m GLU* 1.3 75.1 - - - +
5032m GLN* 1.3 57.6 + - - +
5033m GLN* 2.7 11.3 + - - +
5035m SER 2.6 19.9 + - - +
5036m SER 3.0 6.4 + - - -
----------------------------------------------------------
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