Contacts of the helix formed by residues 1247 - 1261 (chain B) in PDB entry 1AIS
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 PRO1247 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A PRO* 4.1 19.7 - - + +
132A GLU* 4.2 18.4 - - + -
1206B VAL 5.3 6.3 - - - +
1208B PRO* 4.4 22.3 - - + +
1211B TYR* 3.8 33.2 - - + +
1245B LYS 3.7 3.8 - - - +
1246B SER* 1.3 85.4 - - - +
1248B ALA* 1.3 57.5 + - - +
1250B LEU* 3.3 6.2 + - + +
1251B VAL* 2.9 33.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1248 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A GLU* 6.0 3.8 - - + +
1171B THR* 4.9 14.4 - - + -
1211B TYR* 5.4 2.6 - - + -
1215B PHE* 4.9 3.6 - - + -
1246B SER* 3.3 4.4 - - - +
1247B PRO* 1.3 80.0 - - - +
1249B GLY* 1.3 58.4 + - - +
1251B VAL* 3.2 11.5 - - - +
1252B ALA* 3.0 31.4 + - - +
1275B ALA* 3.6 26.4 - - + +
1277B VAL* 3.8 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1249 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1246B SER* 3.3 17.1 + - - -
1248B ALA* 1.3 79.4 - - - +
1250B LEU* 1.3 60.0 + - - +
1252B ALA* 3.6 4.5 + - - +
1253B ALA 3.2 16.5 + - - -
1277B VAL* 4.0 4.6 - - - +
1281B THR* 4.0 24.2 - - - +
1282B VAL* 5.0 0.9 - - - -
1285B ARG* 3.2 21.5 - - - +
1429E T 4.5 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1250 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1208B PRO* 4.7 15.0 - - + -
1233B LEU* 3.6 14.7 - - + +
1236B ALA* 5.7 0.2 - - + -
1241B LEU 4.5 6.5 - - - +
1242B THR* 3.8 38.1 - - + +
1245B LYS* 3.7 30.5 - - + +
1246B SER 3.3 11.6 + - - +
1247B PRO* 3.3 6.6 + - + +
1249B GLY* 1.3 73.2 - - - +
1251B VAL* 1.3 61.1 + - - +
1253B ALA* 3.4 2.7 + - - +
1254B ALA* 3.0 28.9 + - - +
1285B ARG* 3.8 20.6 - - + -
1288B GLU* 5.3 2.0 - - - +
1289B LEU* 4.2 20.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1251 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1208B PRO* 3.8 18.1 - - + +
1211B TYR* 4.2 6.7 - - + -
1212B VAL* 3.7 36.3 - - + +
1215B PHE* 3.7 21.5 - - + -
1233B LEU* 4.2 10.0 - - + +
1247B PRO 2.9 22.2 + - - +
1248B ALA* 3.2 14.6 - - - +
1250B LEU* 1.3 74.0 - - - +
1252B ALA* 1.3 63.8 + - - +
1254B ALA* 3.8 0.2 - - - +
1255B LEU* 2.9 41.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1252 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1248B ALA 3.0 19.8 + - - +
1249B GLY 3.7 4.9 - - - +
1250B LEU 3.2 0.2 - - - -
1251B VAL* 1.3 78.9 - - - +
1253B ALA* 1.3 56.2 + - - +
1255B LEU* 4.6 1.8 - - - -
1256B TYR* 2.9 26.1 + - - +
1271B VAL* 3.0 27.0 - - + +
1275B ALA* 3.7 19.7 - - + -
1277B VAL* 4.1 3.4 - - + -
1282B VAL* 3.9 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1253 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1249B GLY 3.2 4.6 + - - +
1250B LEU 3.8 0.9 - - - +
1251B VAL 3.4 0.2 - - - -
1252B ALA* 1.3 77.2 - - - +
1254B ALA* 1.3 60.0 + - - +
1256B TYR* 3.3 6.8 + - - +
1257B ILE* 2.8 36.9 + - - +
1282B VAL* 4.2 5.5 - - + +
1285B ARG* 3.5 18.8 - - + -
1286B TYR* 3.3 38.1 - - + +
1289B LEU* 3.8 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1254 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1229B ALA* 3.8 13.0 - - + +
1232B ILE* 3.8 21.8 - - + +
1233B LEU* 3.6 30.7 - - + -
1250B LEU 3.0 18.3 + - - +
1251B VAL 3.8 3.6 - - - +
1253B ALA* 1.3 75.5 - - - +
1255B LEU* 1.3 58.5 + - - +
1257B ILE* 3.2 2.7 + - - +
1258B ALA* 2.8 31.7 + - - +
1289B LEU* 4.0 2.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1255 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1212B VAL* 4.3 14.8 - - + +
1215B PHE* 3.5 36.1 - - + -
1216B ALA* 4.3 12.1 - - + +
1219B LEU* 4.2 16.6 - - + -
1225B VAL* 4.3 17.2 - - + +
1226B ARG* 5.1 0.2 - - - -
1229B ALA* 3.9 20.4 - - + -
1251B VAL* 2.9 34.7 + - + +
1252B ALA* 3.7 4.9 - - - +
1254B ALA* 1.3 74.7 - - - +
1256B TYR* 1.3 63.4 + - - +
1258B ALA* 3.8 1.4 - - - +
1259B SER* 3.0 25.5 + - - -
1271B VAL* 4.4 9.0 - - + -
1274B VAL* 5.7 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1256 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1252B ALA 2.9 19.5 + - - +
1253B ALA* 3.5 5.8 - - - +
1254B ALA 3.2 0.2 - - - -
1255B LEU* 1.3 76.1 - - - +
1257B ILE* 1.3 63.1 + - - +
1259B SER* 2.7 22.9 + - - -
1260B LEU* 3.3 33.1 + - + +
1265B LYS* 4.6 13.9 + - - -
1266B ARG 3.2 26.9 - - - -
1267B THR* 4.0 4.0 - - - -
1268B GLN* 3.4 53.5 + - + +
1271B VAL* 4.2 11.6 - - + +
1282B VAL* 4.5 5.4 - - + -
1286B TYR* 3.9 36.4 + + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1257 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1232B ILE* 3.9 10.1 - - + -
1253B ALA 2.8 26.4 + - - +
1254B ALA* 3.7 4.0 - - - +
1256B TYR* 1.3 72.7 - - - +
1258B ALA* 1.3 58.9 + - - +
1260B LEU* 3.3 10.4 + - + +
1261B LEU* 3.0 29.2 + - + +
1286B TYR* 3.8 33.4 - - + +
1289B LEU* 3.7 36.3 - - + -
1290B VAL* 3.8 9.9 - - + -
1295B ILE* 3.9 37.5 - - + -
1297B VAL* 5.3 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1258 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1225B VAL* 3.5 30.7 - - + +
1228B ARG* 3.9 12.8 - - + -
1229B ALA* 3.7 15.3 - - + +
1232B ILE* 4.1 1.5 - - + +
1254B ALA 2.8 17.3 + - - +
1255B LEU 3.8 3.8 - - - +
1257B ILE* 1.3 74.9 - - - +
1259B SER* 1.3 60.3 + - - +
1261B LEU* 4.3 6.3 - - - -
1262B GLU* 2.8 35.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1259 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1225B VAL* 4.2 14.7 - - - +
1255B LEU 3.0 14.6 + - - -
1256B TYR 2.7 19.8 + - - -
1258B ALA* 1.3 75.1 - - - +
1260B LEU* 1.3 60.2 + - - +
1263B GLY 3.2 2.4 + - - -
1264B GLU 2.8 52.9 + - - -
1265B LYS* 3.2 1.3 + - - -
1266B ARG* 3.2 32.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1260 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1256B TYR* 3.3 43.5 + - + +
1257B ILE* 3.3 10.4 + - - +
1258B ALA 3.1 0.4 - - - -
1259B SER* 1.3 81.9 + - - +
1261B LEU* 1.3 66.0 + - - +
1263B GLY* 3.1 14.3 + - - -
1265B LYS* 3.7 37.2 - - + +
1286B TYR* 5.2 4.7 - - + -
1297B VAL* 3.5 31.4 - - + -
1298B PRO* 3.4 26.1 - - + +
1299B ILE 4.5 9.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1261 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1228B ARG* 3.5 43.1 - - + +
1232B ILE* 4.4 2.9 - - + -
1257B ILE* 3.0 28.4 + - + +
1258B ALA* 3.8 4.0 - - - +
1260B LEU* 1.3 76.7 - - - +
1262B GLU* 1.3 65.1 + - - +
1263B GLY 3.5 0.9 + - - -
1295B ILE* 3.8 26.9 - - + -
1296B LYS 3.6 24.9 - - - +
1297B VAL* 4.0 4.0 - - + -
1298B PRO* 3.9 14.9 - - + +
----------------------------------------------------------
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