Contacts of the helix formed by residues 1258 - 1267 (chain J) in PDB entry 3F5P
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 SER1258 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1195J VAL* 4.7 3.8 - - - -
1256J ARG 3.9 0.2 + - - -
1257J PRO* 1.3 75.7 - - - +
1259J PHE* 1.3 60.5 + - - +
1260J LEU* 3.5 10.0 + - - +
1261J GLU* 2.9 36.7 + - - +
1262J ILE* 3.0 29.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1259 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1120J ALA* 3.6 16.5 - - + +
1123J MET* 3.5 54.3 - - + -
1124J ALA* 3.6 21.1 - - + -
1127J ASN* 3.5 29.8 + - + -
1194J ASP* 3.9 19.7 - - + -
1195J VAL* 3.9 18.6 - - + +
1198J PHE* 3.7 30.5 - + + -
1258J SER* 1.3 73.6 - - - +
1260J LEU* 1.3 60.1 + - - +
1262J ILE* 3.6 12.2 + - + +
1263J ILE* 3.0 31.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1260 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1124J ALA* 4.3 13.9 - - + +
1128J ALA* 6.5 0.7 - - + -
1258J SER* 3.1 9.0 + - - +
1259J PHE* 1.3 76.5 - - - +
1261J GLU* 1.3 60.1 + - + +
1263J ILE* 3.1 6.0 + - + +
1264J SER* 2.9 28.5 + - - -
1279J PHE* 4.2 17.0 - - + -
1280J TYR* 3.5 23.7 - - + -
1285J ASN* 3.4 39.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1261 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1256J ARG 4.6 1.0 - - - +
1257J PRO* 3.3 9.5 - - - +
1258J SER* 2.9 37.8 + - - +
1260J LEU* 1.3 72.3 - - + +
1262J ILE* 1.3 66.9 + - - +
1264J SER* 3.1 8.6 + - - -
1265J SER* 3.0 22.9 + - - -
986S VAL* 3.2 31.8 - - + +
987S TYR* 4.1 20.3 - - - +
989S PRO* 5.8 3.8 - - + +
1049S ASN* 6.0 0.5 + - - -
1052S SER* 5.7 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1262 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1116J ALA* 6.0 0.4 - - + -
1120J ALA* 4.5 8.7 - - + -
1195J VAL* 4.7 3.8 - - + -
1198J PHE* 4.0 34.8 - - + -
1244J LEU* 4.0 30.5 - - + -
1248J CYS* 4.2 7.9 - - - -
1257J PRO* 3.7 28.7 - - + +
1258J SER 3.0 24.3 + - - +
1259J PHE* 3.8 15.5 - - + +
1261J GLU* 1.3 73.9 - - - +
1263J ILE* 1.3 62.7 + - - +
1265J SER* 2.7 25.2 + - - -
1266J ILE* 3.4 13.0 - - + +
986S VAL* 4.8 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1263 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1117J GLY* 4.3 5.2 - - - +
1120J ALA* 3.7 17.3 - - + +
1121J ASP* 3.5 42.6 - - + +
1124J ALA* 4.3 6.3 - - + -
1259J PHE 3.0 23.1 + - - +
1260J LEU* 3.1 7.4 + - - +
1262J ILE* 1.3 73.9 - - - +
1264J SER* 1.3 56.7 + - - +
1266J ILE* 2.9 11.0 + - + +
1267J LYS* 2.7 36.5 + - + -
1270J MET* 5.7 0.9 - - + -
1274J PHE* 4.0 20.6 - - + -
1280J TYR* 3.8 31.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER1264 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1260J LEU 2.9 12.4 + - - -
1261J GLU* 3.5 11.6 + - - -
1263J ILE* 1.3 77.2 - - - +
1265J SER* 1.3 62.0 + - - +
1266J ILE 3.3 0.5 + - - -
1267J LYS* 3.3 25.4 - - - +
1268J GLU* 5.0 0.3 - - - +
1280J TYR* 3.3 26.1 + - - -
985S ASP 5.0 3.5 + - - -
986S VAL 5.6 1.3 + - - -
988S VAL 5.0 3.6 + - - -
989S PRO* 5.4 1.8 - - - +
990S ASP* 3.7 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1265 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1244J LEU* 5.1 1.2 - - - +
1261J GLU 3.0 10.6 + - - -
1262J ILE* 2.7 22.4 + - - +
1263J ILE 3.1 0.4 - - - -
1264J SER* 1.3 77.9 + - - +
1266J ILE* 1.3 63.4 + - - +
1267J LYS 3.7 0.2 - - - -
1268J GLU* 5.5 0.6 - - - +
1269J GLU* 4.8 4.7 - - - +
981S PHE* 3.3 35.7 - - - -
985S ASP* 3.3 27.1 - - - +
986S VAL* 3.8 7.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1266 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1113J ILE* 3.8 24.5 - - + +
1116J ALA* 4.3 8.1 - - + -
1117J GLY* 3.5 37.5 - - - +
1240J MET* 3.9 27.4 - - + -
1244J LEU* 4.9 4.9 - - + -
1262J ILE* 3.4 20.4 - - + +
1263J ILE* 2.9 12.7 + - + +
1265J SER* 1.3 91.0 - - - +
1267J LYS* 1.3 67.5 + - - +
1268J GLU 3.3 2.7 - - - -
1269J GLU* 2.9 25.1 + - + +
1270J MET* 3.5 10.9 - - - +
981S PHE* 4.5 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1267 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1263J ILE* 2.7 21.8 + - + +
1264J SER* 3.3 19.1 - - - +
1265J SER 3.7 0.2 - - - -
1266J ILE* 1.3 72.1 - - - +
1268J GLU* 1.3 96.0 + - - +
1270J MET* 3.0 30.4 + - - +
1274J PHE* 5.2 2.2 - - + -
1280J TYR* 3.7 29.5 + - + +
1281J TYR* 3.4 33.3 + - + +
990S ASP* 2.5 39.4 + - - -
----------------------------------------------------------
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