Contacts of the helix formed by residues 1384 - 1393 (chain H) in PDB entry 6BAA
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 GLY1384 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1362H LEU* 3.7 8.1 - - - +
1380H ARG* 4.2 6.1 - - - +
1383H SER* 1.3 82.0 - - - +
1385H LYS* 1.3 59.1 + - - +
1386H SER 3.5 0.9 - - - -
1387H SER 4.0 1.1 - - - -
1388H PHE* 3.0 33.4 + - - +
1552H LEU* 4.0 17.8 - - - +
1555H GLY* 3.7 17.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1385 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1377H ILE* 4.8 13.0 - - + +
1380H ARG* 5.1 5.5 - - - +
1381H THR 4.7 12.6 - - - +
1382H GLY* 4.5 1.2 - - - -
1384H GLY* 1.3 74.7 - - - +
1386H SER* 1.3 58.8 + - - +
1388H PHE* 3.8 4.2 - - - +
1389H SER* 2.9 29.7 + - - -
1536H ILE* 4.6 20.3 - - + +
1537H ALA 4.8 6.5 - - - +
1552H LEU* 3.6 22.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1386 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1382H GLY* 3.7 21.2 + - - -
1385H LYS* 1.3 76.9 - - - +
1387H SER* 1.3 61.7 + - - +
1389H SER* 3.7 6.0 - - - -
1390H LEU* 2.8 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1387 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1352H VAL* 4.6 4.4 - - - +
1354H TYR* 5.6 5.6 - - - -
1361H VAL* 3.7 24.0 - - - -
1362H LEU* 3.7 29.0 - - - +
1382H GLY 4.2 3.3 + - - -
1383H SER 4.0 9.9 - - - -
1384H GLY 3.6 1.8 + - - -
1385H LYS 3.4 0.2 - - - -
1386H SER* 1.3 74.5 - - - +
1388H PHE* 1.3 60.7 + - - +
1390H LEU* 3.4 7.2 + - - +
1391H ALA* 3.0 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1388 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1362H LEU* 3.7 16.2 - - + +
1365H VAL* 5.7 6.5 - - + -
1384H GLY 3.0 20.0 + - - +
1385H LYS* 3.8 4.7 - - - +
1387H SER* 1.3 74.3 - - - +
1389H SER* 1.3 60.1 + - - +
1391H ALA* 3.3 5.5 + - - +
1392H PHE* 2.9 26.7 + - - +
1552H LEU* 6.1 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER1389 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1385H LYS 2.9 19.2 + - - -
1386H SER* 3.7 7.2 - - - -
1388H PHE* 1.3 75.8 - - - +
1390H LEU* 1.3 52.0 + - - +
1392H PHE* 2.9 8.4 + - - +
1393H PHE* 2.6 57.6 + - - -
1504H ILE* 5.9 2.7 - - - -
1536H ILE* 5.3 10.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1390 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1354H TYR* 3.2 26.9 - - + +
1386H SER 2.8 22.1 + - - +
1387H SER* 3.6 8.5 - - - +
1389H SER* 1.3 73.0 - - - +
1391H ALA* 1.3 56.1 + - - +
1393H PHE* 3.4 6.0 - - - -
1394H ARG 2.8 6.8 + - - -
1395H MET* 2.5 41.4 + - + -
1396H VAL* 4.5 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1391 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1350H LEU* 6.3 2.5 - - + -
1352H VAL* 5.6 6.3 - - + -
1362H LEU* 4.8 9.0 - - + -
1387H SER 3.0 14.0 + - - +
1388H PHE* 3.6 10.8 - - - +
1390H LEU* 1.3 71.9 - - - +
1392H PHE* 1.3 61.8 + - - +
1394H ARG* 3.0 17.5 + - - +
1396H VAL* 4.1 16.3 - - - +
1398H MET* 5.9 5.8 - - + +
1403H ILE* 4.9 18.1 - - + +
1410H ILE* 5.9 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1392 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1388H PHE 2.9 14.2 + - - +
1389H SER* 3.2 12.1 - - - +
1391H ALA* 1.3 76.2 - - - +
1393H PHE* 1.3 66.6 + + - +
1394H ARG* 3.3 2.1 + - - +
1404H ILE 5.5 4.0 - - - -
1405H ILE* 4.6 20.6 - - + -
1410H ILE* 5.9 2.6 - - - +
1419H ARG* 5.9 0.5 - - - +
1422H LEU* 5.6 11.2 - - + -
1423H SER 6.0 0.9 - - - -
1424H ILE* 5.5 3.1 - - + -
1502H ILE* 3.8 30.5 - - + -
1503H PHE 4.6 6.3 - - - -
1504H ILE* 3.6 34.5 - - + -
1534H VAL* 5.4 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1393 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511H LEU* 4.8 21.8 - - + -
1389H SER* 2.6 44.9 + - - +
1390H LEU* 3.8 7.6 - - - +
1392H PHE* 1.3 75.3 - + - +
1394H ARG* 1.3 68.1 + - - +
1395H MET* 3.5 4.9 + - + +
1419H ARG* 4.2 12.2 - - - +
1424H ILE* 3.6 24.9 - - + -
1504H ILE* 3.7 28.9 - - + -
----------------------------------------------------------
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