Contacts of the helix formed by residues 1238 - 1249 (chain S) 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 PRO1238 (chain S).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1109S LEU* 3.7 47.1 - - + +
1112S MET* 4.7 16.4 - - + -
1206S ALA* 5.9 0.2 - - + -
1236S ASN 3.5 6.9 - - - +
1237S CYS* 1.3 103.1 - - - +
1239S ASP* 1.3 66.8 + - - +
1240S MET* 3.2 5.4 + - + +
1241S LEU* 4.4 6.7 - - + +
1242S PHE* 3.6 6.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1239 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1233S LYS* 3.2 28.1 + - - +
1237S CYS 4.1 2.6 - - - +
1238S PRO* 1.3 73.0 - - - +
1240S MET* 1.3 65.7 + - - +
1242S PHE* 3.7 3.1 + - - +
1243S GLU* 3.4 25.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET1240 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1109S LEU* 4.2 19.3 - - + -
1113S ILE* 3.3 38.4 - - + -
1238S PRO* 3.1 4.2 - - + -
1239S ASP* 1.3 74.1 - - - +
1241S LEU* 1.3 61.3 + - + +
1242S PHE 3.0 1.3 - - - -
1243S GLU* 2.6 30.8 + - - +
1244S LEU* 3.1 23.4 + - + -
1266S ILE* 3.5 26.0 - - + -
981T PHE* 3.7 45.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1241 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1109S LEU* 4.7 4.0 - - + -
1112S MET* 3.8 46.0 - - + -
1113S ILE* 3.6 30.3 - - + -
1116S ALA* 4.9 3.6 - - + -
1202S LEU* 4.2 25.0 - - + +
1205S ILE* 5.6 1.6 - - + -
1206S ALA* 4.7 4.5 - - + -
1237S CYS* 4.0 18.2 - - - -
1238S PRO* 3.6 10.3 + - + +
1240S MET* 1.3 84.5 - - + +
1242S PHE* 1.3 56.3 + - - +
1244S LEU* 3.4 12.8 - - + +
1245S MET* 3.2 36.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1242 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1203S TRP* 5.4 0.2 - + - -
1230S LEU* 6.3 2.2 - - + -
1231S LEU 4.0 15.7 - - - -
1232S ASP* 4.1 1.6 - - - -
1233S LYS* 3.3 70.0 - - + -
1234S PRO* 3.9 1.3 - - + -
1237S CYS* 4.0 7.7 - - - -
1238S PRO 3.6 2.6 + - - +
1239S ASP 4.0 6.5 - - - +
1240S MET 2.9 1.2 + - - -
1241S LEU* 1.3 76.7 - - - +
1243S GLU* 1.3 72.2 + - - +
1245S MET* 3.4 20.7 - - - +
1246S ARG* 3.1 46.2 + - + +
1249S TRP* 4.3 11.7 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1243 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1233S LYS* 5.9 0.2 + - - -
1239S ASP* 3.4 18.2 + - - +
1240S MET* 2.6 20.1 + - - +
1242S PHE* 1.3 79.2 - - - +
1244S LEU* 1.3 65.8 + - - +
1246S ARG* 2.4 53.5 + - - +
1247S MET* 3.0 26.1 + - + +
981T PHE* 4.6 17.7 - - + +
982T SER* 4.7 4.7 - - - -
1041T MET* 3.9 14.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1244 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1116S ALA* 5.3 2.5 - - + -
1198S PHE* 5.1 0.4 - - + -
1202S LEU* 4.1 18.6 - - + -
1240S MET* 3.1 27.1 + - + +
1241S LEU* 3.4 20.0 - - + +
1243S GLU* 1.3 76.4 - - - +
1245S MET* 1.3 61.4 + - - +
1247S MET* 3.2 25.4 + - + +
1248S CYS* 3.1 23.4 + - - -
1257S PRO* 5.2 0.9 - - + -
1262S ILE* 3.6 42.4 - - + -
1265S SER* 5.0 0.7 - - - +
1266S ILE* 4.7 11.0 - - + -
981T PHE* 4.2 14.1 - - + -
986T VAL* 4.7 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET1245 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1199S GLY* 3.9 10.8 - - - +
1202S LEU* 3.6 21.3 - - + +
1203S TRP* 3.4 36.3 - - - +
1206S ALA* 4.0 14.6 - - + -
1234S PRO* 4.4 2.0 - - + -
1237S CYS* 4.2 11.2 - - - -
1241S LEU* 3.2 19.0 + - + +
1242S PHE* 3.4 28.5 - - - +
1243S GLU 3.1 0.4 - - - -
1244S LEU* 1.3 80.8 - - - +
1246S ARG* 1.3 57.2 + - - +
1248S CYS* 3.0 7.4 + - - +
1249S TRP* 2.9 66.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1246 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1230S LEU* 5.0 16.1 - - + +
1242S PHE* 3.1 42.4 + - + +
1243S GLU* 2.4 51.0 + - - +
1245S MET* 1.3 76.0 - - - +
1247S MET* 1.3 60.9 + - - +
1249S TRP* 3.5 14.9 + - + +
1250S GLN* 3.2 19.6 + - - +
1041T MET* 3.7 41.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET1247 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1243S GLU* 3.0 21.1 + - + +
1244S LEU* 3.3 17.7 - - - +
1246S ARG* 1.3 77.0 - - - +
1248S CYS* 1.3 63.0 + - - +
1249S TRP 3.1 1.0 + - - -
1250S GLN* 3.2 22.1 + - - +
1256S ARG* 3.6 1.4 - - - +
1257S PRO* 3.5 26.1 - - + +
981T PHE* 3.5 32.3 - - + -
982T SER 3.8 20.0 - - - +
983T ALA* 3.9 4.9 - - - +
986T VAL* 3.5 22.4 - - - -
987T TYR* 3.9 23.6 + - + +
1041T MET* 3.3 22.9 - - + -
1045T ILE* 4.5 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS1248 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1195S VAL* 3.7 21.1 - - - +
1196S TRP* 3.4 14.0 - - - -
1198S PHE* 3.9 19.3 - - - -
1199S GLY* 3.7 20.9 - - - -
1202S LEU* 5.0 0.7 - - - -
1244S LEU* 3.1 16.4 + - - +
1245S MET 3.0 8.3 + - - +
1247S MET* 1.3 78.5 - - - +
1249S TRP* 1.3 58.8 + - - +
1250S GLN 3.4 0.9 - - - -
1256S ARG* 3.3 19.8 + - - -
1257S PRO* 4.1 4.0 - - - -
1262S ILE* 3.8 29.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP1249 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1196S TRP* 3.2 65.3 + + + -
1199S GLY* 3.2 29.7 - - - -
1200S VAL* 3.5 10.8 - - + +
1203S TRP* 4.0 6.5 - + + -
1213S TYR* 5.8 0.7 - - - -
1230S LEU* 3.7 37.9 - - + +
1231S LEU* 3.8 44.4 - - + -
1242S PHE* 4.3 8.5 - + - -
1245S MET* 2.9 52.5 + - + +
1246S ARG* 3.5 11.2 + - + +
1247S MET 3.1 1.0 - - - -
1248S CYS* 1.3 82.1 - - - +
1250S GLN* 1.3 66.6 + - - +
1251S TYR* 3.1 3.5 + - - -
----------------------------------------------------------
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