Contacts of the helix formed by residues 1421 - 1430 (chain B) in PDB entry 3PT6
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 SER1421 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
660B GLU* 5.0 7.4 - - - +
1419B ASP 3.9 0.6 + - - -
1420B MET* 1.3 77.4 - - - +
1422B PRO* 1.3 62.8 - - - +
1423B LEU* 2.9 21.7 + - - +
1424B VAL* 3.1 22.0 + - - +
1425B ALA* 2.6 35.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO1422 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1420B MET 3.8 1.5 - - - +
1421B SER* 1.3 87.4 - - - +
1423B LEU* 1.3 52.3 + - - +
1425B ALA* 3.0 9.3 + - + +
1426B ALA* 2.8 35.0 + - - +
1449B LEU* 4.6 8.7 - - + +
1450B GLY* 4.8 4.8 + - - +
1451B ASP* 3.9 39.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1423 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
660B GLU* 5.7 3.6 - - + +
1421B SER* 2.9 8.8 + - - +
1422B PRO* 1.3 78.3 - - - +
1424B VAL* 1.3 66.2 + - + +
1426B ALA* 3.0 15.9 + - - +
1427B ARG* 3.2 45.7 + - + +
1449B LEU* 3.9 33.0 - - + +
1455B ALA* 5.2 1.8 - - + -
1495B SER* 3.7 32.8 - - - +
1496B THR 3.8 10.8 - - - +
1497B LEU* 4.7 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1424 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
660B GLU* 3.5 36.3 - - + +
1420B MET* 3.7 33.4 - - + -
1421B SER* 3.0 23.7 + - - +
1423B LEU* 1.3 76.5 - - + +
1425B ALA* 1.3 64.1 + - - +
1427B ARG* 3.0 17.6 + - - +
1428B MET* 3.1 15.7 + - + +
1516B TYR* 3.6 26.2 - - + +
1534B PRO* 4.3 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1425 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1382B ASN* 4.4 19.7 - - + +
1420B MET* 4.4 1.1 - - - +
1421B SER 2.6 20.4 + - - +
1422B PRO* 3.3 9.9 - - + +
1424B VAL* 1.3 73.2 - - - +
1426B ALA* 1.3 63.9 + - - +
1428B MET* 3.5 18.0 + - + +
1429B ARG* 3.4 21.7 + - - +
1547B HIS* 4.8 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1426 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1422B PRO 2.8 12.0 + - - +
1423B LEU 3.0 10.5 + - - +
1425B ALA* 1.3 76.9 - - - +
1427B ARG* 1.3 62.2 + - - +
1429B ARG* 3.1 31.8 + - - +
1430B HIS* 3.1 20.7 - - + -
1447B VAL* 4.8 6.3 - - + -
1449B LEU* 3.7 23.6 - - + -
1450B GLY 6.0 0.7 - - - +
1497B LEU* 4.2 11.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1427 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
660B GLU* 3.5 15.8 + - - -
1423B LEU* 3.2 35.2 + - - +
1424B VAL* 3.0 10.7 + - - +
1426B ALA* 1.3 80.0 - - - +
1428B MET* 1.3 58.0 + - - +
1430B HIS* 2.9 20.6 + - - +
1431B ILE* 3.2 18.1 + - - +
1442B LEU* 3.8 11.0 - - + +
1496B THR* 3.3 19.2 + - - +
1497B LEU* 2.9 39.2 + - + +
1499B PRO* 3.5 24.1 - - - +
1516B TYR* 2.7 52.2 + - + -
1535B MET* 3.5 17.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET1428 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1382B ASN* 3.5 28.5 - - - +
1420B MET* 3.6 19.1 - - + -
1424B VAL* 3.1 10.4 + - + +
1425B ALA* 3.8 15.9 - - - +
1426B ALA 3.3 0.2 - - - -
1427B ARG* 1.3 75.8 - - - +
1429B ARG* 1.3 60.5 + - - +
1430B HIS 3.5 0.2 + - - -
1431B ILE* 3.6 3.0 + - - +
1516B TYR* 4.4 10.8 - - + -
1518B ARG* 3.1 25.5 + - - -
1534B PRO* 4.6 1.8 - - - -
1542B LEU* 3.5 42.4 - - + -
1547B HIS* 3.6 28.0 + - - +
1548B ARG* 3.8 14.1 - - - -
1549B VAL* 4.0 9.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1429 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1425B ALA 3.4 8.8 + - - +
1426B ALA* 3.1 34.9 + - - +
1427B ARG 3.1 0.2 - - - -
1428B MET* 1.3 80.1 - - - +
1430B HIS* 1.3 90.6 + - + +
1431B ILE 3.5 3.5 + - - +
1447B VAL* 4.1 15.4 - - - +
1448B ARG 5.6 1.2 + - - -
1450B GLY 5.9 2.6 - - - +
1547B HIS* 3.4 44.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS1430 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1426B ALA* 3.1 24.4 + - + +
1427B ARG 2.9 10.3 + - - +
1429B ARG* 1.3 107.0 + - - +
1431B ILE* 1.3 58.7 + - - +
1432B PRO* 3.2 12.3 - - - +
1442B LEU* 3.9 16.1 - - + +
1443B PRO* 3.9 20.5 - - + +
1445B ILE* 4.1 24.0 - - + +
1447B VAL* 3.9 12.8 - - + +
1497B LEU* 4.1 19.3 - - + -
----------------------------------------------------------
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