Contacts of the helix formed by residues 1314 - 1335 (chain C) in PDB entry 3B13
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 ASP1314 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1308C TYR* 3.1 11.5 + - + +
1312C ILE* 3.4 24.9 - - + +
1313C PHE* 1.3 75.0 - - - +
1315C TYR* 1.3 58.3 + - - +
1316C GLU* 3.3 10.2 + - - +
1317C LEU* 3.0 43.4 + - + +
1318C LEU* 3.0 24.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1315 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1295A GLU* 6.0 0.7 - - - -
1329A TYR* 3.5 51.9 - + + +
1330A GLU* 4.7 0.7 - - - +
1332A ILE* 4.6 14.4 - - + -
1333A MET* 3.8 28.0 - - + -
1420A ARG* 4.7 8.5 + - - -
1421A PHE* 5.5 1.6 - - - -
1430A ILE* 3.5 39.2 - - + +
1308C TYR 4.2 12.3 - - - -
1309C GLU* 4.4 14.7 + - + +
1313C PHE* 3.8 24.8 + + - -
1314C ASP* 1.3 76.2 + - - +
1316C GLU* 1.3 62.7 + - - +
1318C LEU* 3.6 8.9 - - + +
1319C SER* 2.9 29.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1316 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1330A GLU* 2.9 35.2 - - - +
1333A MET* 5.0 8.5 - - + +
1334A LYS* 4.7 7.6 - - - +
1314C ASP* 3.3 7.5 + - - +
1315C TYR* 1.3 75.1 - - - +
1317C LEU* 1.3 68.6 + - + +
1319C SER* 3.3 4.8 + - - -
1320C GLN* 3.0 56.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1317 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1278C GLU* 3.4 26.0 - - - +
1282C GLU* 5.0 4.5 - - - +
1308C TYR* 3.4 31.3 - - + +
1312C ILE* 5.2 1.8 - - + -
1314C ASP* 3.0 32.2 + - + +
1316C GLU* 1.3 77.9 - - + +
1318C LEU* 1.3 63.3 + - - +
1320C GLN* 3.4 23.9 + - + +
1321C ASN* 2.9 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1318 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1302A LYS* 6.2 0.2 - - - +
1329A TYR* 3.4 47.8 - - + -
1305C ALA* 3.8 36.8 - - + +
1308C TYR* 3.9 9.4 - - + -
1309C GLU* 3.7 26.9 - - + +
1314C ASP 3.0 18.7 + - - +
1315C TYR* 3.7 10.3 - - + +
1316C GLU 3.1 0.2 - - - -
1317C LEU* 1.3 75.8 - - - +
1319C SER* 1.3 65.5 + - - +
1321C ASN* 2.8 15.3 + - - +
1322C LEU* 2.9 24.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1319 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1326A ALA* 2.9 36.9 + - - +
1329A TYR* 4.5 2.2 - - - +
1330A GLU* 3.6 24.3 + - - +
1315C TYR 2.9 22.1 + - - -
1316C GLU* 3.6 5.8 + - - -
1318C LEU* 1.3 74.7 - - - +
1320C GLN* 1.3 62.0 + - - +
1322C LEU* 3.2 5.1 + - - +
1323C ILE* 3.0 33.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1320 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1316C GLU* 3.0 47.9 + - - +
1317C LEU* 3.7 21.1 - - - +
1319C SER* 1.3 73.0 - - - +
1321C ASN* 1.3 68.3 + - - +
1323C ILE* 3.2 12.7 + - + +
1324C GLN* 2.9 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1321 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1285C ILE* 5.8 0.2 - - - +
1301C CYS* 3.4 29.6 + - - +
1304C LEU* 3.7 21.4 - - - +
1305C ALA* 3.1 27.9 - - + +
1308C TYR* 4.1 7.3 - - + -
1317C LEU 2.9 13.7 + - - +
1318C LEU* 2.8 17.1 + - - +
1320C GLN* 1.3 72.1 - - - +
1322C LEU* 1.3 57.6 + - - +
1324C GLN* 3.1 7.6 + - - +
1325C GLN* 2.9 46.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1322 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1302A LYS* 5.9 3.1 - - - +
1322A LEU* 3.8 37.7 - - + +
1325A GLN* 3.6 33.0 - - + +
1326A ALA* 3.9 8.7 - - + +
1329A TYR* 3.7 26.0 - - + -
1305C ALA* 5.1 2.0 - - + -
1318C LEU* 2.9 26.1 + - + +
1319C SER* 3.5 7.9 - - - +
1321C ASN* 1.3 74.6 - - - +
1323C ILE* 1.3 66.2 + - - +
1325C GLN* 3.3 19.2 + - - +
1326C ALA* 3.0 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1323 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1323A ILE* 5.0 17.7 - - + +
1326A ALA* 3.6 17.7 - - + -
1319C SER* 3.0 23.0 + - - +
1320C GLN* 3.2 11.4 + - + +
1322C LEU* 1.3 75.4 - - - +
1324C GLN* 1.3 58.2 + - - +
1326C ALA* 3.2 8.1 + - - +
1327C LYS* 3.0 25.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1324 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1285C ILE* 4.3 11.1 - - - +
1289C ASP* 4.5 4.8 + - - -
1301C CYS* 4.4 6.2 - - - -
1320C GLN 2.9 16.1 + - - +
1321C ASN* 3.1 6.3 + - - +
1323C ILE* 1.3 76.9 - - + +
1325C GLN* 1.3 64.0 + - - +
1327C LYS* 3.3 26.2 + - + +
1328C PHE* 2.9 66.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1325 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1322A LEU* 3.8 16.1 - - + +
1298C ILE* 3.9 13.4 - - + +
1301C CYS* 3.6 21.9 - - + -
1302C LYS* 3.7 35.4 - - - +
1305C ALA* 4.1 6.5 - - - +
1321C ASN* 2.9 33.9 + - - +
1322C LEU* 3.6 18.9 - - - +
1324C GLN* 1.3 74.6 - - - +
1326C ALA* 1.3 65.9 + - - +
1328C PHE* 2.8 19.0 + - - +
1329C TYR* 3.0 30.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1326 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1319A SER* 3.0 30.4 + - - +
1322A LEU* 3.9 11.5 - - + +
1323A ILE* 3.5 32.5 - - + -
1322C LEU 3.0 12.5 + - - +
1323C ILE 3.3 9.9 - - - +
1325C GLN* 1.3 78.1 - - - +
1327C LYS* 1.3 62.5 + - - +
1329C TYR* 3.4 1.7 + - - +
1330C GLU* 3.0 20.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1327 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1289C ASP* 4.2 12.4 + - - -
1294C TRP* 6.2 0.2 - - - +
1323C ILE* 3.0 14.3 + - + +
1324C GLN* 3.7 33.6 - - + +
1325C GLN 3.2 0.4 - - - -
1326C ALA* 1.3 76.6 - - - +
1328C PHE* 1.3 70.6 + - + +
1330C GLU* 3.4 7.9 + - - +
1331C SER* 2.9 41.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1328 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1285C ILE* 4.1 8.5 - - + -
1289C ASP* 3.4 32.8 - - + -
1294C TRP* 3.4 23.4 - + + +
1297C ALA* 3.5 28.3 - - + -
1298C ILE* 3.3 31.4 - - + -
1301C CYS* 4.1 13.5 - - - -
1324C GLN* 2.9 54.3 + - - -
1325C GLN* 2.8 6.3 + - - +
1327C LYS* 1.3 87.7 - - + +
1329C TYR* 1.3 56.6 + - - +
1331C SER* 3.0 6.3 + - - -
1332C ILE* 2.9 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1329 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1309A GLU* 3.3 26.5 + - + -
1315A TYR* 3.7 56.5 - + + +
1318A LEU* 3.4 24.6 - - + +
1319A SER* 4.6 2.2 - - - -
1322A LEU* 3.8 23.1 - - + -
1298C ILE* 3.3 40.5 - - + +
1302C LYS* 4.5 1.9 - - - -
1325C GLN* 3.0 30.3 + - - -
1326C ALA 3.9 4.5 - - - +
1328C PHE* 1.3 72.1 - - - +
1330C GLU* 1.3 67.1 + - - +
1331C SER 3.2 0.2 + - - -
1332C ILE* 3.3 8.9 + - + +
1333C MET* 3.0 25.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1330 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1315A TYR 5.6 0.9 - - - -
1316A GLU* 2.6 32.1 - - - +
1319A SER* 3.4 23.5 + - - +
1323A ILE* 6.4 0.2 - - + -
1326C ALA 3.0 13.6 + - - +
1327C LYS* 3.5 9.2 - - - +
1329C TYR* 1.3 75.7 - - - +
1331C SER* 1.3 58.9 + - - +
1333C MET* 3.0 8.9 + - - +
1334C LYS* 2.8 64.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1331 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1294C TRP* 3.7 36.7 + - - -
1327C LYS* 2.9 30.7 + - - +
1328C PHE* 3.0 10.6 + - - -
1330C GLU* 1.3 74.4 - - - +
1332C ILE* 1.3 67.3 + - - +
1335C ILE* 2.9 43.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1332 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1315A TYR* 4.3 27.4 - - + -
1294C TRP* 3.7 23.3 - - + -
1295C GLU* 3.3 33.0 - - + +
1298C ILE* 4.4 14.8 - - + -
1328C PHE 2.9 15.5 + - - +
1329C TYR* 3.5 9.6 - - + +
1331C SER* 1.3 75.4 - - - +
1333C MET* 1.3 59.8 + - - +
1335C ILE 4.4 3.6 - - - +
1337C ARG* 3.8 22.4 + - - +
1429C GLN* 3.1 27.3 + - - +
1430C ILE* 4.7 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET1333 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1313A PHE 4.7 2.7 - - - +
1315A TYR* 3.5 41.3 - - + +
1316A GLU* 4.8 5.4 - - + +
1329C TYR 3.0 9.1 + - - +
1330C GLU* 3.4 12.6 - - - +
1331C SER 3.0 0.6 - - - -
1332C ILE* 1.3 79.8 - - - +
1334C LYS* 1.3 67.2 + - + +
1427C PRO* 4.9 5.4 - - + -
1429C GLN* 2.6 47.7 + - + +
1430C ILE* 3.2 40.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1334 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1316A GLU* 4.0 10.7 + - - -
1330C GLU* 2.8 47.4 + - - +
1331C SER* 5.5 0.2 - - - -
1333C MET* 1.3 80.6 - - + +
1335C ILE* 1.3 65.7 + - + +
1336C LEU 4.2 0.7 + - - -
1429C GLN* 5.2 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1335 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1292C LYS* 5.3 3.6 - - + -
1294C TRP* 3.5 26.9 - - + -
1331C SER* 2.9 33.0 + - - +
1332C ILE 4.4 5.7 - - - +
1333C MET 3.6 0.8 - - - -
1334C LYS* 1.3 85.1 - - + +
1336C LEU* 1.3 76.6 + - + +
1337C ARG* 3.5 9.9 + - - +
1429C GLN* 4.8 5.5 + - - -
----------------------------------------------------------
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