Contacts of the helix formed by residues 146 - 159 (chain 2) in PDB entry 6Q8W
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 THR 146 (chain 2).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4371 TRP* 4.0 3.6 - - - -
4381 ARG* 2.3 39.4 + - - +
1442 CYS 2.9 11.3 + - - +
1452 VAL* 1.3 74.1 - - - +
1472 ARG* 1.3 55.5 + - - +
1482 ALA* 3.8 10.8 + - + +
1492 ARG* 3.1 29.1 + - + +
1502 LEU* 2.6 37.9 + - - +
1692 PRO* 5.3 5.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 147 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4351 SER* 5.1 3.0 + - - -
4371 TRP* 2.4 78.3 + - + +
4381 ARG* 2.8 23.3 + - - +
992 TYR* 5.1 9.2 - - + -
1462 THR* 1.3 78.3 + - - +
1482 ALA* 1.3 56.9 + - - +
1502 LEU* 3.7 1.5 - - - +
1512 GLU* 2.9 58.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 148 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4381 ARG* 4.7 0.4 + - - -
1462 THR* 3.2 10.7 + - + +
1472 ARG* 1.3 77.3 - - - +
1492 ARG* 1.3 59.8 + - - +
1512 GLU* 3.4 6.5 + - - +
1522 ALA* 2.9 32.4 + - - +
1692 PRO* 4.2 16.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 149 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1422 VAL* 3.6 16.3 - - + +
1432 GLU 3.0 22.3 + - - +
1442 CYS* 3.2 22.8 + - - +
1452 VAL* 4.4 3.6 - - - -
1462 THR* 3.1 24.2 + - + +
1482 ALA* 1.3 78.0 - - - +
1502 LEU* 1.3 57.1 + - - +
1522 ALA* 3.9 0.7 - - - +
1532 LEU* 2.9 32.4 + - - +
1682 LEU* 3.3 53.0 - - + +
1692 PRO* 3.1 34.3 + - + +
1702 GLY* 4.5 8.5 + - - -
1712 LYS 5.6 0.2 - - - -
1722 CYS* 3.6 26.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 150 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4371 TRP* 4.7 4.3 - - + -
962 LEU* 3.9 25.6 - - + -
992 TYR* 3.6 34.1 - - + -
1002 LEU* 4.7 8.5 - - + -
1342 ILE* 4.6 10.1 - - + -
1452 VAL* 3.8 18.7 - - + +
1462 THR 2.6 21.8 + - - +
1472 ARG* 3.7 4.7 - - - +
1492 ARG* 1.3 73.6 - - - +
1512 GLU* 1.3 64.9 + - + +
1532 LEU* 3.5 11.8 - - + +
1542 LEU* 2.9 49.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 151 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
992 TYR* 3.7 24.5 + - - +
1472 ARG* 2.9 44.9 + - - +
1482 ALA* 4.0 5.6 - - - +
1502 LEU* 1.3 83.6 - - + +
1522 ALA* 1.3 57.6 + - - +
1542 LEU* 3.3 7.5 + - + +
1552 ALA* 2.9 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 152 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1482 ALA 2.9 18.8 + - - +
1492 ARG 3.9 2.5 - - - +
1512 GLU* 1.3 74.5 - - - +
1532 LEU* 1.3 60.4 + - - +
1552 ALA* 3.4 5.5 + - - +
1562 GLY* 2.9 27.0 + - - -
1662 ILE* 4.7 5.4 - - - +
1672 GLU 4.4 9.4 - - - +
1682 LEU* 5.4 1.1 - - + -
1692 PRO* 4.3 19.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 153 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
802 LEU* 5.2 7.6 - - + -
1342 ILE* 5.7 7.2 - - + -
1362 VAL* 5.2 4.5 - - + -
1422 VAL* 4.5 29.8 - - + -
1492 ARG 2.9 19.5 + - - +
1502 LEU* 3.5 13.9 - - + +
1522 ALA* 1.3 75.8 - - - +
1542 LEU* 1.3 68.2 + - + +
1562 GLY 3.9 0.3 - - - -
1572 LEU* 2.9 71.5 + - + +
1632 LEU* 4.6 6.7 - - + -
1662 ILE* 4.1 19.2 - - + +
1682 LEU* 4.7 9.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 154 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
802 LEU* 4.7 11.9 - - + -
992 TYR* 5.8 1.8 - - + -
1002 LEU* 4.1 21.8 - - + -
1032 THR* 6.0 4.0 - - + -
1042 LEU* 5.1 8.1 - - + -
1172 PHE* 4.0 34.2 - - + -
1502 LEU* 2.9 37.3 + - + +
1512 GLU* 3.6 8.5 - - + +
1522 ALA 3.2 0.2 - - - -
1532 LEU* 1.3 88.9 - - + +
1552 ALA* 1.3 56.4 + - - +
1572 LEU* 3.5 3.1 + - + +
1582 ARG* 2.9 52.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 155 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1512 GLU 2.9 16.3 + - - +
1522 ALA* 4.0 5.2 - - - +
1542 LEU* 1.3 73.4 - - - +
1562 GLY* 1.3 60.5 + - - +
1582 ARG* 3.2 13.1 + - - +
1592 ALA* 2.9 30.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 156 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1522 ALA 2.9 16.9 + - - -
1532 LEU 3.9 0.4 - - - -
1552 ALA* 1.3 76.5 - - - +
1572 LEU* 1.3 58.2 + - - +
1592 ALA* 3.1 6.3 + - - -
1602 GLY 2.9 11.1 + - - -
1612 LYS* 2.8 47.3 + - - +
1662 ILE* 4.2 6.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 157 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
782 TYR* 4.2 52.5 + - + -
802 LEU* 4.8 2.7 - - + -
1162 LEU* 4.4 4.9 - - - +
1172 PHE* 4.6 18.2 - - + -
1362 VAL* 4.7 11.9 - - + -
1532 LEU* 2.9 47.7 + - + +
1542 LEU* 3.9 4.0 - - + +
1562 GLY* 1.3 74.7 - - - +
1582 ARG* 1.3 61.5 + - - +
1602 GLY* 3.2 11.5 + - - -
1612 LYS 3.6 20.2 - - - +
1632 LEU* 4.6 13.7 - - + +
1662 ILE* 3.9 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 158 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1032 THR* 5.1 8.1 - - - +
1042 LEU* 3.5 29.1 - - - +
1142 ASP* 5.2 6.9 + - - -
1162 LEU* 4.9 6.1 - - + +
1172 PHE* 4.0 25.4 - - + -
1542 LEU* 2.9 40.5 + - - +
1552 ALA* 3.4 11.5 - - - +
1572 LEU* 1.3 77.0 - - - +
1592 ALA* 1.3 56.8 + - - +
1602 GLY 3.7 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 159 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1552 ALA 2.9 15.6 + - - +
1562 GLY* 3.1 6.0 + - - +
1582 ARG* 1.3 75.7 - - - +
1602 GLY* 1.3 60.4 + - - +
1612 LYS* 3.5 4.9 - - + +
----------------------------------------------------------
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