Contacts of the helix formed by residues 1284 - 1294 (chain B) in PDB entry 1FP7
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 SER1284 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1209B LEU 4.5 1.8 - - - -
1210B CYS* 3.5 20.1 - - - +
1271B HIS* 2.6 61.8 + - - +
1272B GLY* 4.9 0.7 - - - -
1283B ASN* 1.3 90.4 - - - +
1285B ILE* 1.3 60.6 - - - +
1286B ILE* 3.3 7.4 - - - -
1287B ALA* 3.1 11.3 - - - +
1288B THR* 3.2 14.0 + - - -
1317B LYS* 3.5 2.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1285 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1209B LEU 4.9 0.2 + - - -
1210B CYS 2.7 16.8 + - - +
1211B LEU* 3.8 26.9 - - + -
1212B ALA 3.7 18.4 - - - +
1213B SER* 5.1 2.7 - - - +
1284B SER* 1.3 72.0 - - - +
1286B ILE* 1.3 61.4 + - + +
1288B THR* 5.1 0.9 - - - -
1289B LYS* 3.2 33.8 + - + +
1317B LYS* 3.2 52.3 - - + +
1320B TYR* 4.5 10.5 - - + -
1321B ALA* 4.1 22.9 - - + -
1323B PHE* 4.3 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1286 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1045B LEU* 5.6 8.1 - - + -
1209B LEU 5.0 5.8 - - - +
1212B ALA 2.9 27.1 - - - +
1213B SER 3.4 18.6 - - - +
1214B ASP* 4.7 3.6 - - - +
1255B ILE* 3.7 20.6 - - + +
1257B PRO* 3.3 41.5 - - + -
1271B HIS* 3.7 20.2 - - + +
1284B SER* 4.2 2.2 - - - -
1285B ILE* 1.3 79.1 - - - +
1287B ALA* 1.3 80.0 + - - +
1289B LYS* 3.4 12.2 - - - +
1290B THR* 3.1 29.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1287 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1095B CYS* 4.5 4.7 - - - -
1257B PRO* 3.8 14.4 - - + -
1269B PHE* 2.9 26.5 - - + +
1271B HIS* 3.7 17.7 - - + +
1283B ASN* 4.5 3.1 - - - +
1284B SER* 3.1 24.1 + - - +
1285B ILE 3.5 0.2 - - - -
1286B ILE* 1.3 88.8 - - - +
1288B THR* 1.3 57.8 + - - +
1290B THR* 4.5 0.2 - - - -
1291B ALA 2.8 22.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR1288 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1059B LEU* 5.4 7.2 - - + -
1095B CYS* 3.2 15.3 - - + +
1283B ASN* 2.9 23.7 + - - -
1284B SER 3.2 8.3 + - - -
1285B ILE 4.9 0.4 - - - -
1287B ALA* 1.3 74.4 - - - +
1289B LYS* 1.3 55.4 + - - +
1290B THR 2.9 2.2 - - - -
1291B ALA* 2.7 4.2 + - - +
1292B LEU* 2.6 39.1 + - + +
1298B VAL* 3.5 27.8 - - + -
1300B THR* 4.9 6.7 - - - -
1317B LYS* 3.2 13.2 + - - +
1323B PHE* 4.6 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1289 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1048B TYR* 3.5 51.9 + - + +
1213B SER* 3.0 38.0 + - - +
1214B ASP* 5.3 1.6 + - - +
1285B ILE* 3.2 28.5 + - + +
1286B ILE* 3.4 15.5 - - - +
1288B THR* 1.3 78.8 - - - +
1290B THR* 1.3 60.0 + - - +
1292B LEU* 3.6 8.2 - - - +
1293B LYS* 3.0 31.4 - - - +
1321B ALA* 6.1 1.3 - - + -
1323B PHE* 3.6 26.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR1290 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1043B ILE* 5.7 1.8 - - + -
1044B SER 5.4 1.4 + - - -
1045B LEU* 5.6 2.3 - - - -
1047B VAL* 4.7 11.1 - - + +
1048B TYR* 3.4 31.1 + - - +
1257B PRO* 5.0 6.3 - - + +
1269B PHE* 3.3 25.6 - - + -
1286B ILE* 3.1 21.2 + - - +
1287B ALA* 3.4 2.2 - - - -
1288B THR 2.9 0.2 - - - -
1289B LYS* 1.3 77.1 - - - +
1291B ALA* 1.3 68.0 + - - +
1293B LYS* 3.0 17.2 + - - +
1294B LEU* 3.3 27.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1291 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1093B MET* 4.1 16.8 - - + +
1095B CYS* 3.6 20.6 - - - -
1269B PHE* 3.8 12.6 - - + -
1287B ALA 2.8 15.8 + - - +
1288B THR 2.7 15.0 + - - +
1290B THR* 1.3 72.5 - - - +
1292B LEU* 1.3 61.3 + - - +
1293B LYS 3.1 1.2 + - - -
1294B LEU* 3.2 12.6 + - - +
1295B ALA* 3.3 12.5 + - - +
1298B VAL* 3.9 18.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1292 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1056B ASP* 2.9 48.2 - - + +
1057B GLY* 3.8 20.5 + - - +
1058B LYS 4.8 4.0 - - - +
1059B LEU* 5.2 11.0 - - + +
1288B THR* 2.6 23.0 + - + +
1289B LYS* 3.6 9.0 - - + +
1290B THR 3.1 0.2 + - - -
1291B ALA* 1.3 72.1 - - - +
1293B LYS* 1.3 57.2 + - - +
1295B ALA 2.8 19.9 - - - +
1298B VAL* 3.4 27.3 - - + +
1323B PHE* 3.9 37.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1293 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1047B VAL* 6.4 0.2 - - + -
1048B TYR* 3.8 28.5 - - + +
1051B LEU* 3.5 45.3 - - + +
1052B LYS 4.1 8.4 + - - -
1054B LYS* 3.6 22.2 + - + -
1055B PRO 3.9 12.9 - - - +
1056B ASP* 2.7 36.7 + - - +
1091B ARG* 5.1 5.0 + - - -
1289B LYS* 3.0 22.2 - - - +
1290B THR* 3.0 6.4 + - - +
1292B LEU* 1.3 71.9 - - - +
1294B LEU* 1.3 53.3 - - + +
1295B ALA* 2.3 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1294 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1026B LEU* 3.0 59.1 - - + +
1027B GLY 4.7 3.1 - - - +
1028B ILE* 4.4 17.5 - - + -
1043B ILE* 5.1 1.8 - - + -
1047B VAL* 3.5 26.9 - - + -
1051B LEU* 4.5 12.1 - - + -
1091B ARG* 4.1 12.6 + - - -
1093B MET* 4.2 8.5 - - - -
1269B PHE* 4.2 12.1 - - + -
1290B THR* 3.5 33.7 - - + +
1291B ALA 3.2 7.1 + - - +
1293B LYS* 1.3 74.7 - - + +
1295B ALA* 1.3 61.1 + - - +
----------------------------------------------------------
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