Contacts of the helix formed by residues 1271 - 1282 (chain A) in PDB entry 6AGF
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 MET1271 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
667A VAL* 5.4 7.2 - - + -
1181A LEU* 4.2 29.2 - - + +
1182A PHE* 4.0 25.4 - - + -
1253A ALA 4.0 13.0 - - - +
1254A VAL* 4.3 10.8 - - + +
1268A ASN* 2.7 61.0 + - - +
1269A LEU 3.3 1.2 - - - -
1270A TYR* 1.3 73.1 - - - +
1272A TYR* 1.3 52.4 + - - +
1273A LEU 2.4 20.2 + - - -
1274A TYR* 2.4 28.0 + - - +
1275A PHE* 3.8 5.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1272 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
741A ARG* 4.7 19.5 + - - -
742A TRP* 4.4 17.0 - + - -
748A PHE* 4.4 7.6 - + + -
749A HIS* 5.2 3.5 - + - -
752A LEU* 3.9 41.3 - - + -
1250A MET* 4.2 39.1 - - + +
1251A TYR* 4.2 19.0 - + - -
1254A VAL* 3.5 25.9 - - + +
1266A GLU* 4.7 4.0 + - - -
1269A LEU* 3.4 36.3 - - + -
1270A TYR 3.2 0.6 - - - -
1271A MET* 1.3 77.1 - - - +
1273A LEU* 1.3 56.6 + - - +
1274A TYR 3.2 0.2 - - - -
1275A PHE* 3.2 15.2 + - - +
1276A VAL* 3.0 28.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1273 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
748A PHE* 4.3 23.1 - - + -
751A PHE* 4.9 2.2 - - + -
1270A TYR* 3.4 25.1 + - + +
1271A MET 2.4 11.1 + - - -
1272A TYR* 1.3 69.8 - - - +
1274A TYR* 1.3 58.5 + - - +
1276A VAL* 3.5 15.0 - - + +
1277A ILE* 2.8 40.8 + - + +
1913A 6OU 3.8 53.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1274 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1174A PHE* 2.3 48.2 + + + +
1177A MET* 3.6 38.4 - - + -
1178A GLY* 3.6 11.0 + - - -
1181A LEU* 4.3 11.7 - - + -
1182A PHE* 3.9 26.5 - + + -
1227A TYR* 3.9 17.4 + - - -
1237A LEU* 4.1 12.6 - - + +
1270A TYR 4.7 0.2 + - - -
1271A MET* 2.4 31.6 + - - +
1273A LEU* 1.3 69.2 - - - +
1275A PHE* 1.3 77.3 - + + +
1277A ILE* 4.0 6.7 - - + +
1278A PHE* 3.2 23.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1275 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1182A PHE* 4.4 8.5 - + - -
1227A TYR* 4.1 8.7 - + - -
1237A LEU* 6.5 0.4 - - + -
1240A VAL* 3.8 28.5 - - + -
1249A ILE* 4.0 25.1 - - + -
1250A MET* 3.6 43.7 - - + -
1253A ALA* 3.7 32.1 - - + -
1254A VAL* 5.6 0.9 - - + -
1271A MET* 4.1 13.5 - - + -
1272A TYR* 3.2 14.4 + + - +
1274A TYR* 1.3 97.2 - + - +
1276A VAL* 1.3 61.9 + - - +
1278A PHE* 4.1 5.1 - + - +
1279A ILE* 3.3 31.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1276 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
751A PHE* 5.0 6.3 - - + -
752A LEU* 4.6 14.6 - - + -
755A PHE* 3.7 41.6 - - + -
1250A MET* 6.2 1.6 - - + -
1272A TYR 3.0 21.8 + - - +
1273A LEU* 3.7 14.6 - - + +
1274A TYR 3.2 0.2 - - - -
1275A PHE* 1.3 76.3 - - + +
1277A ILE* 1.3 63.7 + - - +
1279A ILE* 3.5 2.6 + - - +
1280A ILE* 3.3 28.9 + - + +
1913A 6OU 4.2 30.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1277 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1174A PHE* 4.2 15.5 - - + -
1177A MET* 6.5 0.9 - - + -
1273A LEU* 2.8 25.7 + - + +
1274A TYR* 4.0 6.7 - - + +
1276A VAL* 1.3 77.1 - - - +
1278A PHE* 1.3 61.7 + - - +
1280A ILE* 3.5 5.0 + - - -
1281A PHE* 3.1 44.2 + - + +
1913A 6OU 4.2 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1278 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1171A TRP* 3.9 31.6 - + - -
1174A PHE* 3.7 32.9 - + + -
1237A LEU* 3.5 54.5 - - + -
1240A VAL* 3.8 19.3 - - + -
1241A ALA* 3.8 21.5 - - + -
1274A TYR* 3.2 20.7 + - + +
1275A PHE* 4.1 4.0 - - - +
1276A VAL 3.3 0.2 - - - -
1277A ILE* 1.3 78.3 - - - +
1279A ILE* 1.3 58.8 + - + +
1282A GLY* 2.6 45.6 + - - -
1283A SER* 3.6 5.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1279 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
755A PHE* 4.0 24.0 - - + -
759A CYS* 4.3 0.7 - - - -
1240A VAL* 4.0 20.4 - - + +
1243A PHE* 3.7 31.0 - - + -
1246A TRP* 3.8 21.5 - - + -
1250A MET* 5.1 0.2 - - + -
1275A PHE* 3.3 22.4 + - + +
1276A VAL 4.0 3.6 - - - +
1277A ILE 3.3 0.2 - - - -
1278A PHE* 1.3 79.9 - - + +
1280A ILE* 1.3 62.9 + - - +
1283A SER* 3.3 12.5 - - - +
1284A PHE* 3.2 20.8 + - - +
1910A 6OU 3.8 26.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1280 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
755A PHE* 4.6 8.1 - - + -
1276A VAL* 3.3 23.7 + - + +
1277A ILE* 3.5 4.9 + - - +
1278A PHE 3.3 0.4 - - - -
1279A ILE* 1.3 78.6 - - - +
1281A PHE* 1.3 68.9 + - + +
1284A PHE* 3.3 22.2 - - + +
1285A PHE* 3.3 21.4 + - + -
1910A 6OU 3.7 57.4 - - + -
1913A 6OU 4.0 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1281 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
693A ILE* 3.9 31.9 - - + -
1170A PHE* 3.4 28.2 - + + -
1174A PHE* 4.0 8.1 - + + -
1277A ILE* 3.1 42.5 + - + +
1280A ILE* 1.3 89.6 - - + +
1282A GLY* 1.3 64.7 + - - +
1283A SER 3.2 2.7 + - - -
1285A PHE* 3.6 34.8 - + - +
1286A THR 3.5 16.6 + - - -
1910A 6OU 6.5 0.4 - - + -
1913A 6OU 6.4 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1282 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1170A PHE* 3.8 12.5 - - - -
1171A TRP* 3.0 37.3 + - - -
1278A PHE* 2.6 30.0 + - - -
1281A PHE* 1.3 74.9 - - - +
1283A SER* 1.3 60.3 + - - -
1286A THR* 3.4 13.7 - - - +
1910A 6OU 4.2 0.7 - - - +
----------------------------------------------------------
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