Contacts of the helix formed by residues 156 - 161 (chain 6) in PDB entry 3J7Y
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 GLY 156 (chain 6).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1526 ALA 2.9 6.3 + - - -
1536 GLU* 3.2 10.1 + - - -
1546 TYR 3.3 1.2 + - - -
1556 TYR* 1.3 77.1 - - - +
1576 LEU* 1.3 59.7 + - - +
1586 TYR 3.5 1.8 - - - -
1596 ARG* 3.4 35.8 + - - +
1606 ASP* 3.1 31.0 + - - +
2676 ARG* 3.3 4.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 157 (chain 6).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1526 ALA* 3.2 17.7 + - + +
1556 TYR* 3.5 29.6 - - + +
1566 GLY* 1.3 75.4 - - - +
1586 TYR* 1.3 64.2 + - + +
1616 LEU* 2.7 46.3 + - + +
1626 PHE* 5.0 0.4 - - - -
2216 LEU* 3.7 24.2 - - + -
2676 ARG* 4.8 4.3 - - + +
2696 ALA* 3.6 31.2 - - + -
3166 LEU* 6.0 6.1 - - + -
3186 PHE* 3.2 43.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 158 (chain 6).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1486 LYS 4.7 0.2 + - - -
1496 GLN* 3.5 23.5 - - + +
1526 ALA* 3.3 34.9 + - + +
1536 GLU* 3.9 14.6 - - + -
1566 GLY* 3.5 0.4 - - - -
1576 LEU* 1.3 80.7 - - + +
1596 ARG* 1.3 56.8 + - - +
1626 PHE* 3.3 12.3 - + - -
1636 HIS 3.2 7.8 + - - -
1646 GLY* 2.8 29.4 + - - +
1656 ALA 4.0 14.6 - - - +
1666 THR* 3.5 33.2 - - + -
1676 PHE* 2.6 58.8 + + - -
1696 PRO* 4.0 7.3 - - - +
3166 LEU* 4.1 8.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 159 (chain 6).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1536 GLU 4.9 3.0 + - - -
1546 TYR 4.8 2.0 + - - -
1566 GLY* 3.4 34.7 + - - +
1576 LEU 3.3 0.6 - - - -
1586 TYR* 1.3 78.3 - - - +
1606 ASP* 1.3 64.8 + - + +
1636 HIS* 3.3 20.3 + - - -
1646 GLY* 3.7 9.5 + - - +
2676 ARG* 5.6 1.3 - - - +
50P ARG* 3.8 26.5 + - - +
52P PRO* 3.7 21.6 - - - +
99P LYS* 5.6 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 160 (chain 6).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1566 GLY 3.1 18.6 + - - +
1596 ARG* 1.3 83.3 - - + +
1616 LEU* 1.3 65.7 + - - +
1626 PHE 3.5 0.2 - - - -
1636 HIS* 4.1 5.5 + - - -
2216 LEU* 2.9 29.6 - - + +
2296 ASP* 5.4 1.2 - - - -
2316 GLU* 3.8 9.5 - - - +
2676 ARG* 3.1 18.1 + - - +
3016 PHE* 5.3 2.8 - - - +
50P ARG* 2.7 36.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 161 (chain 6).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1576 LEU* 2.7 34.1 + - + +
1606 ASP* 1.3 76.9 - - - +
1626 PHE* 1.3 73.4 + - + +
2196 THR* 3.8 9.6 - - - +
2216 LEU* 4.0 11.0 - - + -
2316 GLU* 3.1 31.2 - - - +
2696 ALA* 4.3 9.2 - - + -
2716 LEU* 3.4 31.4 - - + -
3006 THR* 2.6 50.8 + - + +
3016 PHE* 3.5 15.6 + - - +
3166 LEU* 5.2 2.2 - - + -
----------------------------------------------------------
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