Contacts of the helix formed by residues 1340 - 1358 (chain M) in PDB entry 2JA7
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 GLY1340 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1335M ILE 3.7 1.2 + - - -
1336M MET 3.4 13.0 + - - -
1338M VAL 3.5 1.8 + - - -
1339M LEU* 1.3 79.8 - - - +
1341M ILE* 1.3 54.2 + - - -
1342M GLU* 2.5 6.5 + - - +
1343M ALA* 2.5 35.5 + - - +
1344M GLY 4.1 3.4 - - - -
150Q VAL* 4.6 1.0 - - - +
153Q HIS* 6.2 0.2 - - - -
182Q ASP* 3.3 18.8 - - - -
183Q PRO* 3.8 4.7 - - - +
184Q VAL* 4.3 5.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1341 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1336M MET* 3.6 25.1 + - + +
1340M GLY* 1.3 68.2 - - - +
1342M GLU* 1.3 66.8 + - + +
1344M GLY* 2.5 23.7 + - - +
1345M ARG* 2.5 18.8 + - - +
1376M THR* 3.7 25.1 - - - +
1379M GLY 2.7 38.6 - - - +
1380M GLY* 3.7 11.7 - - - +
1381M LEU* 6.3 0.7 - - + -
153Q HIS* 5.5 1.1 - - - +
177Q ARG 4.3 9.6 - - - +
178Q ILE* 4.5 10.8 - - + -
182Q ASP* 3.0 27.4 + - - +
212Q ARG* 3.9 16.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1342 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1340M GLY 2.5 6.2 + - - +
1341M ILE* 1.3 80.5 - - + +
1343M ALA* 1.3 60.2 + - - +
1345M ARG* 3.4 13.8 + - - +
1346M ALA* 3.2 18.7 + - - +
150Q VAL* 5.6 0.2 - - + -
151Q PRO* 3.9 19.4 - - + +
153Q HIS* 3.7 17.3 - - + +
198Q ILE* 3.2 36.3 - - + +
200Q ARG* 3.0 39.3 + - - -
210Q SER* 4.7 5.8 + - - -
212Q ARG* 2.3 33.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1343 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1335M ILE* 4.0 2.6 - - + +
1339M LEU* 3.9 13.7 - - + -
1340M GLY 2.5 17.4 + - - +
1342M GLU* 1.3 72.1 - - - +
1344M GLY* 1.3 68.4 - - - +
1346M ALA* 3.2 10.6 + - - +
1347M ALA* 3.0 15.2 + - - +
149Q LEU* 3.6 28.3 - - + +
150Q VAL* 3.4 29.6 - - + +
151Q PRO* 4.5 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1344 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1332M PHE* 4.5 4.0 - - - +
1335M ILE* 4.1 14.0 + - - +
1336M MET* 4.2 20.4 - - - -
1340M GLY 3.5 2.4 + - - -
1341M ILE* 2.5 17.9 + - - +
1343M ALA* 1.3 73.7 - - - +
1345M ARG* 1.3 62.7 + - - -
1347M ALA* 2.7 14.7 + - - +
1348M LEU* 2.7 16.8 + - - +
1381M LEU* 5.9 4.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1345 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
870M GLU* 3.6 9.1 + - - -
1341M ILE* 2.5 13.5 + - - +
1342M GLU* 3.4 18.9 + - - +
1344M GLY* 1.3 72.3 - - - +
1346M ALA* 1.3 74.7 + - - +
1348M LEU* 2.9 7.8 + - - +
1349M TYR* 2.7 32.1 + - - +
1365M TYR* 3.0 26.3 + - - -
1369M ALA* 4.4 3.0 - - - +
1372M VAL* 3.8 19.9 - - + +
1373M ASP* 2.4 45.5 + - - -
1376M THR* 3.6 32.0 - - + +
1381M LEU* 6.0 0.8 - - - +
200Q ARG* 3.1 38.2 - - - +
212Q ARG* 5.8 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1346 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1342M GLU 3.2 9.6 + - - +
1343M ALA* 3.2 14.3 + - - +
1345M ARG* 1.3 86.9 - - - +
1347M ALA* 1.3 57.4 + - - +
1349M TYR* 3.6 7.5 + - - +
1350M LYS* 2.9 28.3 + - - +
149Q LEU* 4.2 24.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1347 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1328M TYR* 3.8 31.8 + - + +
1332M PHE* 3.9 17.5 - - + -
1335M ILE* 4.0 12.1 - - + -
1343M ALA 3.0 9.6 + - - +
1344M GLY 2.7 13.2 + - - +
1346M ALA* 1.3 68.6 - - - +
1348M LEU* 1.3 67.8 + - - +
1349M TYR 2.9 1.6 - - - -
1350M LYS* 2.7 6.0 + - - -
1351M GLU* 2.7 26.3 + - - +
149Q LEU* 4.3 4.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1348 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1104M ILE* 3.5 20.6 - - + -
1332M PHE* 3.5 37.5 - - + +
1344M GLY 2.7 15.2 + - - +
1345M ARG* 3.4 11.7 - - - +
1347M ALA* 1.3 72.1 - - - +
1349M TYR* 1.3 59.0 + - - +
1351M GLU* 4.0 4.0 - - + +
1352M VAL* 2.9 35.1 + - + +
1372M VAL* 3.2 28.9 - - + +
1375M MET* 3.8 32.5 - - + -
1376M THR* 5.3 1.1 - - - -
1381M LEU* 3.9 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1349 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1345M ARG* 2.7 26.3 + - - +
1346M ALA* 3.6 6.5 - - - +
1347M ALA 2.7 0.6 + - - -
1348M LEU* 1.3 71.2 - - - +
1350M LYS* 1.3 83.7 + - + +
1352M VAL* 2.7 18.5 + - - +
1353M TYR* 2.8 35.9 + + + +
1365M TYR* 3.7 36.8 - + - -
1368M MET* 3.1 49.1 - - + +
1369M ALA* 4.1 20.2 - - + -
1372M VAL* 3.2 19.2 - - + +
203Q GLU* 3.8 12.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1350 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1119M TYR* 5.6 4.0 + - - -
1328M TYR* 3.8 40.4 - - + +
1346M ALA 2.9 16.1 + - - +
1347M ALA* 2.7 8.6 + - - +
1349M TYR* 1.3 88.1 - - + +
1351M GLU* 1.3 58.5 + - - +
1353M TYR* 3.4 5.6 + - + +
1354M ASN* 2.6 44.7 + - - +
148Q GLU* 5.7 2.8 + - - -
149Q LEU* 5.9 9.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1351 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1094M VAL* 5.6 5.7 - - - +
1100M ARG* 2.8 42.7 + - - +
1104M ILE* 3.9 10.5 - - + -
1328M TYR* 2.8 29.3 + - - +
1330M ASN* 3.1 28.8 + - - +
1332M PHE* 5.5 3.1 - - + -
1347M ALA 2.7 18.5 + - - +
1348M LEU* 4.0 5.6 - - - +
1349M TYR 2.8 1.2 + - - -
1350M LYS* 1.3 73.1 - - - +
1352M VAL* 1.3 63.7 + - - +
1354M ASN* 2.9 25.6 + - - +
1355M VAL* 3.2 13.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1352 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1072M ILE* 5.1 3.8 - - + -
1101M LEU* 5.1 13.0 - - + -
1104M ILE* 3.8 31.6 - - + +
1105M LEU* 5.8 1.1 - - + -
1348M LEU* 2.9 26.2 + - + +
1349M TYR* 2.7 14.0 + - - +
1351M GLU* 1.3 72.9 - - - +
1353M TYR* 1.3 62.9 + - - +
1355M VAL* 3.2 18.4 + - + +
1356M ILE* 3.5 14.3 + - + +
1368M MET* 4.5 23.3 - - + +
1371M LEU* 4.7 20.0 - - + -
1372M VAL* 4.9 4.3 - - + -
1375M MET* 6.0 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1353 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1349M TYR* 2.8 41.4 + + + +
1350M LYS* 3.6 13.5 - - + +
1352M VAL* 1.3 72.4 - - - +
1354M ASN* 1.3 76.0 + - - +
1356M ILE* 3.1 6.4 + - + +
1357M ALA* 3.0 37.5 + - + +
1361M SER 6.1 0.9 - - - -
1362M TYR* 5.8 8.5 - + - -
1363M VAL 5.6 3.6 - - - -
1368M MET* 4.0 27.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1354 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1328M TYR* 5.9 1.4 - - - -
1350M LYS* 2.6 43.0 + - - +
1351M GLU* 2.9 20.8 + - - +
1353M TYR* 1.3 91.9 - - - +
1355M VAL* 1.3 56.4 + - + +
1357M ALA* 4.1 7.5 - - - +
1358M SER* 2.9 34.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1355 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1079M MET* 4.0 22.1 - - + +
1096M SER 4.5 2.9 - - - +
1097M GLY* 3.8 24.4 - - - -
1100M ARG* 3.8 26.9 - - + +
1101M LEU* 3.8 27.1 - - + +
1104M ILE* 3.9 13.0 - - + -
1351M GLU* 3.5 14.1 - - + +
1352M VAL* 3.2 9.6 + - - +
1354M ASN* 1.3 77.4 - - + +
1356M ILE* 1.3 61.3 + - + +
1358M SER* 3.1 17.3 + - - -
1359M ASP 4.4 1.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1356 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1072M ILE* 4.0 29.4 - - + +
1075M PRO* 4.8 7.9 - - + -
1079M MET* 5.5 7.2 - - + -
1101M LEU* 6.2 2.2 - - + -
1352M VAL* 3.7 12.6 - - + +
1353M TYR* 3.1 9.4 + - + +
1355M VAL* 1.3 81.0 - - + +
1357M ALA* 1.3 60.9 + - - +
1358M SER 3.5 0.2 - - - -
1359M ASP* 4.0 5.5 + - - +
1361M SER* 3.4 40.4 + - - +
1362M TYR 4.5 0.2 - - - +
1363M VAL* 3.9 29.4 - - + +
1368M MET* 3.4 32.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1357 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1353M TYR* 3.0 38.5 + - + +
1354M ASN* 3.1 11.6 + - - +
1356M ILE* 1.3 75.8 - - - +
1358M SER* 1.3 54.0 + - - +
1359M ASP 2.9 5.2 - - - -
1360M GLY* 2.8 25.1 + - - -
1361M SER 4.3 8.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1358 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1096M SER* 5.1 3.3 - - - -
1097M GLY* 4.8 10.3 + - - -
1354M ASN 2.9 14.3 + - - -
1355M VAL* 3.1 21.0 + - - -
1357M ALA* 1.3 76.3 - - - +
1359M ASP* 1.3 59.5 + - - +
1360M GLY 3.3 0.2 - - - -
----------------------------------------------------------
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