Contacts of the helix formed by residues 1374 - 1399 (chain A) in PDB entry 6AH0
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 PRO1374 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1210A LYS 6.0 2.2 - - - +
1211A ASP* 5.9 6.5 - - - +
1276A GLU* 5.0 9.9 - - - -
1372A ILE 4.1 1.6 - - - -
1373A GLN* 1.3 74.5 - - - +
1375A TRP* 1.3 64.8 + - - +
1376A GLU 3.3 3.1 - - - -
1377A SER* 3.2 7.5 + - - +
1378A GLU* 3.1 17.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP1375 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1211A ASP* 6.3 0.2 - - - +
1276A GLU* 4.8 11.3 - - - +
1373A GLN 3.8 1.9 + - - -
1374A PRO* 1.3 72.1 - - - +
1376A GLU* 1.3 56.3 + - - +
1378A GLU* 3.2 3.3 + - - +
1379A PHE* 2.8 27.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1376 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1213A VAL 5.8 2.0 + - - -
1214A TRP* 5.3 13.8 - - - +
1215A ASN 5.6 2.5 - - - +
1374A PRO 3.3 0.8 - - - -
1375A TRP* 1.3 76.6 - - - +
1377A SER* 1.3 62.1 + - - +
1379A PHE* 3.2 2.4 + - - +
1380A ILE* 3.0 20.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER1377 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1374A PRO* 3.2 8.8 + - - +
1376A GLU* 1.3 77.2 - - - +
1378A GLU* 1.3 56.7 + - - +
1380A ILE* 3.3 2.1 + - - -
1381A ASP* 3.0 24.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1378 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1373A GLN 5.8 0.4 - - - -
1374A PRO 3.1 13.3 + - - -
1375A TRP* 3.2 3.8 + - - +
1377A SER* 1.3 73.2 - - - +
1379A PHE* 1.3 60.6 + - - +
1381A ASP* 3.2 2.2 + - - +
1382A SER* 2.9 25.5 + - - -
1415A GLY* 5.1 2.6 + - - -
1416A ILE* 4.9 6.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1379 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1375A TRP 2.8 15.0 + - - -
1376A GLU* 3.2 3.3 + - - +
1378A GLU* 1.3 75.7 - - - +
1380A ILE* 1.3 61.6 - - - +
1382A SER* 3.2 2.4 + - - +
1383A GLN* 3.1 19.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1380 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1376A GLU 3.0 13.6 + - - -
1377A SER 3.8 3.1 - - - -
1379A PHE* 1.3 77.0 - - - +
1381A ASP* 1.3 60.9 - - - +
1383A GLN* 3.2 3.4 + - - +
1384A ARG* 3.0 19.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1381 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1377A SER 3.0 15.0 + - - -
1378A GLU* 3.2 3.6 + - - +
1380A ILE* 1.3 75.9 - - - +
1382A SER* 1.3 56.4 + - - +
1384A ARG* 3.2 1.2 + - - +
1385A VAL* 2.8 30.8 + - - -
1414A ARG 5.5 0.6 - - - -
1415A GLY* 4.7 7.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1382 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1378A GLU 2.9 14.2 + - - -
1379A PHE* 3.2 3.3 + - - +
1380A ILE 3.2 0.2 - - - -
1381A ASP* 1.3 76.6 - - - +
1383A GLN* 1.3 62.4 + - - +
1386A TRP* 3.1 21.8 + - - +
1415A GLY* 3.8 24.3 - - - -
1416A ILE 4.2 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1383 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1379A PHE 3.1 13.8 + - - -
1380A ILE* 3.2 2.9 + - - +
1382A SER* 1.3 75.9 - - - +
1384A ARG* 1.3 63.6 + - - +
1387A ALA* 3.2 18.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1384 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1380A ILE 3.0 13.9 + - - -
1381A ASP* 3.7 2.0 - - - +
1383A GLN* 1.3 78.0 - - - +
1385A VAL* 1.3 57.3 + - - +
1387A ALA* 3.2 2.8 + - - -
1388A GLU* 2.9 26.2 + - - -
2220A PRO 4.6 14.1 - - - +
2221A GLY* 5.4 2.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1385 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1381A ASP 2.8 19.9 + - - -
1382A SER* 5.2 0.4 - - - +
1384A ARG* 1.3 72.0 - - - +
1386A TRP* 1.3 56.6 + - - +
1388A GLU* 3.2 3.0 + - - +
1389A TYR* 2.9 25.5 + - - -
1411A SER* 6.5 1.1 - - - +
1414A ARG 5.9 4.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP1386 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1382A SER* 3.1 17.1 + - - +
1385A VAL* 1.3 76.2 - - - +
1387A ALA* 1.3 56.8 + - - +
1389A TYR* 3.4 2.1 + - - +
1390A ALA* 3.0 24.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1387 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1383A GLN 3.2 12.7 + - - -
1384A ARG 3.2 7.3 + - - -
1386A TRP* 1.3 77.5 - - - +
1388A GLU* 1.3 60.5 + - - +
1390A ALA* 3.2 2.5 + - - +
1391A LEU* 3.1 19.1 + - - -
2221A GLY 5.9 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1388 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1384A ARG 2.9 14.0 + - - -
1385A VAL* 3.2 3.6 + - - +
1387A ALA* 1.3 75.2 - - - +
1389A TYR* 1.3 57.4 + - - +
1391A LEU* 3.2 3.4 + - - +
1392A LYS* 2.9 25.5 + - - -
2220A PRO 5.6 1.1 - - - -
2221A GLY* 4.6 19.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1389 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1385A VAL 2.9 14.5 + - - -
1386A TRP* 3.4 4.0 + - - +
1388A GLU* 1.3 76.8 - - - +
1390A ALA* 1.3 51.6 + - - +
1392A LYS* 3.2 3.0 + - - +
1393A ARG* 2.8 32.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1390 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1386A TRP 3.0 15.3 + - - -
1387A ALA* 3.2 4.4 + - - +
1389A TYR* 1.3 73.7 - - - +
1391A LEU* 1.3 58.3 + - - +
1393A ARG* 3.2 2.8 + - - +
1394A GLN* 2.9 24.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1391 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1387A ALA 3.1 13.1 + - - -
1388A GLU 3.2 3.3 + - - -
1390A ALA* 1.3 75.8 - - - +
1392A LYS* 1.3 62.9 + - - +
1394A GLN* 3.2 3.4 + - - +
1395A GLU* 3.1 18.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1392 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1388A GLU 2.9 14.7 + - - -
1389A TYR* 3.2 4.4 + - - +
1391A LEU* 1.3 77.7 - - - +
1393A ARG* 1.3 55.3 + - - +
1395A GLU* 3.2 2.4 + - - +
1396A ALA* 2.9 25.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1393 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1389A TYR 2.8 17.5 + - - -
1390A ALA* 3.2 4.7 + - - +
1392A LYS* 1.3 72.5 - - - +
1394A GLN* 1.3 56.1 + - - +
1396A ALA* 3.2 3.0 + - - +
1397A ILE* 2.9 25.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1394 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1390A ALA 2.9 14.4 + - - -
1391A LEU* 3.2 4.2 + - - +
1393A ARG* 1.3 74.2 - - - +
1395A GLU* 1.3 57.1 + - - +
1397A ILE* 3.2 2.7 + - - +
1398A ALA* 2.9 24.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1395 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1391A LEU 3.1 12.8 + - - -
1392A LYS* 3.7 3.6 - - - +
1394A GLN* 1.3 74.5 - - - +
1396A ALA* 1.3 58.9 + - - +
1398A ALA* 3.2 2.9 + - - +
1399A GLN* 2.8 28.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1396 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1392A LYS 2.9 15.1 + - - -
1393A ARG* 3.2 4.7 + - - +
1395A GLU* 1.3 75.7 - - - +
1397A ILE* 1.3 55.9 + - - +
1399A GLN* 3.4 1.4 + - - +
1400A ASN 2.9 22.5 + - - -
1401A ARG* 3.0 28.6 + - - +
1402A ARG 6.2 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1397 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1393A ARG 2.9 13.8 + - - -
1394A GLN* 3.6 3.8 - - - +
1395A GLU 3.2 0.2 - - - -
1396A ALA* 1.3 77.5 - - - +
1398A ALA* 1.3 61.3 + - - +
1400A ASN* 3.1 14.4 + - - +
1401A ARG 5.2 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1398 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1394A GLN 2.9 14.5 + - - -
1395A GLU* 3.2 3.6 + - - +
1397A ILE* 1.3 75.8 - - - +
1399A GLN* 1.3 57.4 + - - +
1400A ASN 3.3 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1399 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1395A GLU 2.8 15.5 + - - -
1396A ALA* 3.5 1.8 - - - +
1398A ALA* 1.3 75.1 - - - +
1400A ASN* 1.3 63.4 + - - +
1401A ARG* 3.4 4.5 + - - -
----------------------------------------------------------
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