Contacts of the helix formed by residues 1320 - 1331 (chain A) in PDB entry 5G04
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 ASN1320 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1274A LEU* 4.8 1.8 - - - -
1318A ASP 5.0 2.0 + - - +
1319A LEU* 1.3 81.4 - - - +
1321A VAL* 1.3 59.4 + - - +
1322A PRO* 3.6 14.8 - - - +
1323A GLU* 3.4 33.5 + - + +
1324A GLN* 3.0 33.5 + - + +
513K THR* 4.2 4.8 + - - -
12W LYS* 3.3 23.3 + - - +
13W LEU* 3.6 21.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1321 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1270A ALA* 5.1 9.6 - - + -
1274A LEU* 3.9 25.1 - - + -
1302A LEU* 4.4 20.6 - - + -
1306A CYS* 5.5 4.9 - - - -
1311A SER 5.5 0.9 - - - +
1313A LEU* 4.3 23.8 - - + -
1316A MET* 5.5 7.6 - - + +
1319A LEU* 4.0 5.8 - - + -
1320A ASN* 1.3 70.7 - - - +
1322A PRO* 1.4 68.7 - - + +
1324A GLN* 4.2 0.4 - - - -
1325A LEU* 3.2 36.9 + - + +
1371A LEU* 5.6 0.2 - - - -
1374A ILE* 4.7 17.5 - - + -
1375A TYR* 4.5 9.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO1322 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1311A SER* 5.2 6.3 - - - +
1320A ASN* 3.6 10.3 - - - +
1321A VAL* 1.4 96.7 - - + +
1323A GLU* 1.3 66.5 + - - +
1325A LEU* 4.5 0.2 - - - +
1326A TYR* 3.2 24.6 + - - +
1371A LEU* 4.7 9.0 - - + -
1375A TYR* 3.2 26.2 - - + +
1383A ILE* 5.1 2.9 - - + -
1386A TRP* 3.8 23.0 - - + -
13W LEU* 3.7 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1323 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1320A ASN* 3.4 37.3 + - + +
1321A VAL 3.4 0.2 - - - -
1322A PRO* 1.3 82.5 - - - +
1324A GLN* 1.3 75.7 + - + +
1326A TYR* 3.6 4.2 - - - +
1327A GLN* 3.1 32.4 + - - +
511K ASP* 3.6 21.0 - - - +
512K ASP* 5.4 0.2 - - - -
513K THR* 2.7 56.1 + - + +
13W LEU* 5.6 3.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1324 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1274A LEU* 3.8 37.0 + - + +
1319A LEU* 5.5 4.9 - - + +
1320A ASN* 3.0 18.0 + - + +
1321A VAL 4.2 0.7 - - - +
1323A GLU* 1.3 89.9 - - + +
1325A LEU* 1.3 58.1 + - - +
1327A GLN* 3.3 18.5 + - - +
1328A TYR* 2.9 64.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1325 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1274A LEU* 3.8 26.0 - - + -
1277A ILE* 4.5 15.9 - - + -
1302A LEU* 4.6 4.9 - - + -
1321A VAL* 3.2 20.7 + - + +
1324A GLN* 1.3 75.1 - - - +
1326A TYR* 1.3 66.1 + - - +
1328A TYR* 3.3 4.2 + - + +
1329A MET* 3.0 28.1 + - - +
1367A ALA* 3.8 16.8 - - - +
1370A ALA* 3.7 26.7 - - + -
1371A LEU* 3.7 35.9 - - + +
1374A ILE* 3.8 18.4 - - + -
1375A TYR* 5.4 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1326 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1322A PRO 3.2 20.0 + - - +
1323A GLU* 3.6 5.8 - - - +
1325A LEU* 1.3 77.3 - - - +
1327A GLN* 1.3 59.3 + - + +
1329A MET* 3.8 3.1 - - - +
1330A VAL* 2.8 71.3 + - + +
1371A LEU* 4.7 1.4 - - - +
1386A TRP* 3.2 59.7 - + + +
513K THR* 5.4 8.7 - - + -
516K VAL* 5.9 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1327 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1323A GLU* 3.1 22.2 + - - +
1324A GLN* 3.3 16.0 + - - +
1326A TYR* 1.3 85.5 - - + +
1328A TYR* 1.3 58.2 + - + +
1330A VAL* 4.4 3.6 - - - -
1331A GLY* 2.9 35.7 + - - +
1332A GLY* 4.4 12.1 - - - +
1333A HIS* 3.7 18.8 - - - +
1358A ILE* 4.0 10.1 - - + +
510K ARG* 2.9 31.3 - - - +
511K ASP* 3.3 26.1 + - - +
513K THR* 5.8 5.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1328 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1274A LEU* 3.5 14.9 + - + -
1275A ALA* 5.2 0.5 - - - -
1277A ILE* 3.6 23.8 - - + -
1278A GLY* 3.4 34.1 + - - -
1324A GLN* 2.9 60.9 + - + +
1325A LEU* 3.9 5.2 - - - +
1326A TYR 3.3 0.2 - - - -
1327A GLN* 1.3 78.0 - - + +
1329A MET* 1.3 61.2 + - - +
1358A ILE* 4.7 19.7 - - + +
1360A VAL* 3.4 13.7 - - - +
1363A THR* 3.2 42.0 + - + +
1364A CYS* 4.0 1.1 - - - -
1367A ALA* 3.9 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET1329 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1325A LEU 3.0 11.8 + - - +
1326A TYR 4.7 3.4 - - - +
1328A TYR* 1.3 77.5 - - - +
1330A VAL* 1.3 67.9 + - - +
1360A VAL* 3.6 7.8 - - - +
1364A CYS* 3.4 27.4 - - - +
1367A ALA* 3.7 10.1 - - + -
1368A THR* 3.7 24.0 - - + +
1371A LEU* 3.3 33.9 - - + -
1386A TRP* 4.3 20.0 - - - +
1387A LEU* 3.6 28.7 - - + -
1407A ARG* 3.7 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1330 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1326A TYR* 2.8 64.4 + - + +
1327A GLN* 4.4 1.1 - - - -
1329A MET* 1.3 86.2 - - + +
1331A GLY* 1.3 69.6 + - - +
1360A VAL* 4.0 4.0 - - - +
1386A TRP 5.8 2.5 - - - +
1398A PHE* 6.1 1.6 - - - -
1407A ARG* 5.0 14.1 - - - +
69L ARG* 5.2 4.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1331 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1327A GLN* 2.9 23.5 + - - +
1329A MET 3.6 1.8 - - - -
1330A VAL* 1.3 89.3 - - - +
1332A GLY* 1.3 57.5 + - - -
1357A THR 4.5 1.8 - - - -
1358A ILE* 4.7 3.8 - - - -
1360A VAL* 3.7 17.2 - - - +
69L ARG* 5.0 9.6 - - - -
----------------------------------------------------------
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