Contacts of the helix formed by residues 1397 - 1404 (chain A) 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 SER1397 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1038A TYR 4.2 6.7 - - - -
1372A ASP* 3.4 40.6 - - - -
1375A SER* 5.1 0.4 - - - -
1395A PRO 3.5 1.0 - - - -
1396A LEU* 1.3 80.0 - - - +
1398A TRP* 1.3 65.4 + - - +
1399A PHE 3.9 2.0 - - - -
1400A GLN* 3.4 19.0 + - - -
1401A ARG* 3.0 34.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP1398 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1038A TYR 4.8 2.0 + - - -
1040A THR 3.6 20.6 + - - +
1041A ASP* 3.7 29.1 - - + -
1042A ILE* 3.6 50.8 - - + +
1043A ASN* 4.8 5.5 + - - -
1079A SER* 6.1 2.2 - - - -
1308A GLY* 5.7 1.3 - - - -
1335A HIS* 4.7 7.0 - + - -
1366A ARG* 6.3 0.7 - - - +
1368A ILE* 4.5 10.5 - - + -
1372A ASP* 5.7 0.6 + - - -
1397A SER* 1.3 71.4 - - - +
1399A PHE* 1.3 102.2 + + + +
1401A ARG* 3.2 19.8 + - - +
1402A GLN* 2.9 61.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1399 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1308A GLY 3.2 27.1 - - - -
1309A VAL* 4.5 6.7 - - + -
1368A ILE* 4.0 17.9 - - + -
1372A ASP* 3.5 34.1 - - + +
1373A THR* 3.8 21.5 - - - -
1397A SER* 3.9 0.2 - - - -
1398A TRP* 1.3 103.0 - + + +
1400A GLN* 1.3 57.3 + - - +
1402A GLN* 3.3 7.5 + - + +
1403A LEU* 3.0 64.5 + - + +
1557A ARG 3.4 21.1 - - - -
1559A GLN 4.3 7.2 - - - -
1560A GLY* 5.2 1.1 - - - -
1585A PRO* 5.5 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1400 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1371A ARG 3.5 1.0 + - - -
1372A ASP 3.2 22.6 + - - +
1373A THR 4.2 1.8 - - - +
1374A MET 4.0 0.8 - - - +
1375A SER* 2.9 37.4 + - - +
1376A ASP* 2.9 34.6 + - - +
1395A PRO* 3.9 12.1 - - + -
1396A LEU* 2.9 20.5 + - - -
1397A SER* 3.3 17.8 + - - +
1398A TRP 3.2 0.4 - - - -
1399A PHE* 1.3 73.4 - - - +
1401A ARG* 1.3 60.8 + - - +
1402A GLN 3.0 1.6 - - - -
1403A LEU* 3.0 6.1 + - - +
1404A ARG* 2.7 36.4 + - - +
1557A ARG* 4.0 10.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1401 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1039A HIS 2.6 32.3 + - - -
1040A THR 3.9 1.2 - - - -
1041A ASP* 2.6 30.4 + - - -
1395A PRO* 3.5 31.2 + - + -
1396A LEU 5.2 0.4 - - - -
1397A SER* 3.0 20.4 + - - +
1398A TRP* 3.4 36.6 - - - +
1400A GLN* 1.3 76.2 - - - +
1402A GLN* 1.3 63.4 + - + +
1405A GLY* 3.2 28.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1402 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1398A TRP* 2.9 63.7 + - + +
1399A PHE* 3.4 10.5 - - + +
1400A GLN 3.0 0.2 - - - -
1401A ARG* 1.3 81.1 + - - +
1403A LEU* 1.3 69.5 + - + +
1405A GLY* 3.5 9.5 + - - -
1562A PRO* 5.7 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1403 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1399A PHE* 3.0 60.1 + - + +
1400A GLN* 3.0 3.8 + - - +
1402A GLN* 1.3 84.9 - - + +
1404A ARG* 1.3 60.1 + - - +
1405A GLY 3.7 0.2 + - - -
1557A ARG* 3.7 24.9 - - + +
1560A GLY* 4.0 20.2 - - - +
1561A PHE 3.6 18.8 - - - +
1562A PRO* 3.8 12.2 - - + +
1563A ASP* 2.9 35.5 + - - +
1564A SER* 4.5 1.2 + - - -
1585A PRO* 6.5 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1404 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1376A ASP* 2.6 41.5 + - - +
1391A TYR* 3.1 51.5 - - + +
1393A GLY 3.4 18.6 + - - -
1394A GLU* 3.8 5.1 + - - +
1395A PRO* 3.7 39.0 - - + +
1400A GLN 2.7 20.0 + - - +
1403A LEU* 1.3 72.8 - - - +
1405A GLY* 1.3 67.5 + - - +
1407A HIS 4.2 10.6 - - - +
1409A GLN* 4.4 12.4 + - - +
1557A ARG* 3.8 7.0 - - - +
1563A ASP* 3.4 24.0 - - - +
----------------------------------------------------------
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