Contacts of the helix formed by residues 1041 - 1055 (chain F) 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 MET1041 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1243E GLU* 2.9 46.9 - - - +
1246E ARG* 3.4 63.6 - - + +
1247E MET* 3.9 19.3 - - + -
1250E GLN* 4.3 5.6 - - - +
983F ALA* 4.8 8.7 - - + +
1040F SER* 1.3 75.4 - - - +
1042F ARG* 1.3 65.3 + - - +
1043F GLU 3.4 0.9 - - - -
1044F ARG* 3.5 5.5 + - - +
1045F ILE* 3.2 38.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1042 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1250E GLN* 3.8 24.0 - - - +
1252E ASN* 5.6 5.5 - - - +
1255E MET* 4.8 12.1 - - - +
1040F SER* 4.3 8.1 - - - +
1041F MET* 1.3 81.1 - - - +
1043F GLU* 1.3 68.7 + - - +
1045F ILE* 3.9 2.1 - - - +
1046F GLU* 3.1 64.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1043 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1010F PHE* 4.0 24.4 - - + +
1039F ALA* 2.9 26.0 - - + +
1040F SER* 2.2 65.7 + - - +
1042F ARG* 1.3 77.5 - - - +
1044F ARG* 1.3 70.8 + - - +
1046F GLU* 3.6 5.9 + - - +
1047F PHE* 2.8 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1044 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
982F SER* 5.0 7.5 - - - -
983F ALA* 4.1 23.8 - - + +
984F ALA* 4.4 7.4 - - - +
1035F VAL* 4.5 23.2 + - + +
1036F ASN 2.9 30.9 + - - -
1037F GLU* 4.0 7.5 + - - +
1039F ALA* 3.3 7.9 + - - -
1040F SER 3.0 21.4 + - - -
1041F MET* 3.5 6.4 + - - +
1042F ARG 3.3 0.6 - - - -
1043F GLU* 1.3 86.9 + - + +
1045F ILE* 1.3 61.9 + - - +
1047F PHE* 3.2 4.7 - - + +
1048F LEU* 2.9 49.8 + - + +
1073F GLN 5.4 2.6 + - - -
1075F THR* 4.1 20.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1045 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1247E MET* 4.3 3.8 - - + -
1250E GLN* 3.9 21.1 - - + +
1255E MET* 3.6 31.2 - - + +
983F ALA* 3.7 19.3 - - + -
987F TYR* 3.5 41.5 - - + +
1041F MET* 3.2 35.6 + - + +
1042F ARG* 3.9 3.1 - - - +
1044F ARG* 1.3 74.3 - - - +
1046F GLU* 1.3 66.0 + - - +
1048F LEU* 3.2 5.3 + - - -
1049F ASN* 2.9 26.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1046 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1255E MET* 4.4 22.7 - - + +
1010F PHE* 4.3 17.2 - - + -
1042F ARG* 3.1 45.1 + - - +
1043F GLU* 3.7 5.2 - - - +
1045F ILE* 1.3 75.3 - - - +
1047F PHE* 1.3 70.1 + - - +
1049F ASN* 3.1 7.2 + - - +
1050F GLU* 3.0 19.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1047 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6F 741 3.7 30.5 - + - -
1010F PHE* 3.2 52.1 - + + -
1033F LYS* 4.2 9.4 - - + -
1035F VAL* 3.4 32.5 - - + -
1043F GLU 2.8 18.8 + - - +
1044F ARG* 3.2 12.3 - - - +
1046F GLU* 1.3 76.5 - - - +
1048F LEU* 1.3 74.1 + - + +
1050F GLU* 3.0 12.0 + - - +
1051F ALA* 3.1 18.6 + - + -
1077F VAL* 3.1 34.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1048 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
983F ALA* 4.0 9.4 - - + +
984F ALA* 3.3 40.6 - - + +
987F TYR* 4.1 19.2 - - + +
988F VAL* 4.0 16.8 - - + +
1035F VAL* 5.5 0.4 - - + -
1044F ARG* 2.9 37.8 + - + +
1045F ILE 3.7 3.6 - - - +
1047F PHE* 1.3 95.9 - - + +
1049F ASN* 1.3 58.8 + - - +
1051F ALA* 3.7 6.8 - - + +
1052F SER* 2.9 25.1 + - - -
1068F VAL* 5.9 2.2 - - + -
1075F THR* 4.8 13.2 - - + -
1077F VAL* 5.9 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1049 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1254E LYS 4.0 9.9 - - - +
1255E MET* 3.6 30.6 - - + +
987F TYR* 3.8 29.8 + - - +
1045F ILE* 2.9 20.9 + - - +
1046F GLU 3.1 5.4 + - - +
1048F LEU* 1.3 78.0 + - - +
1050F GLU* 1.3 66.3 + - - +
1052F SER* 2.9 23.9 + - - -
1053F VAL* 3.4 11.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1050 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6F 741 3.5 27.7 - - + -
1009F SER* 5.4 0.5 + - - -
1010F PHE* 3.9 18.4 - - - -
1046F GLU 3.0 9.7 + - - +
1047F PHE 3.0 10.4 + - - +
1049F ASN* 1.3 74.0 - - - +
1051F ALA* 1.3 56.5 + - - +
1052F SER 2.8 9.9 + - - -
1053F VAL* 2.8 21.0 + - - +
1054F MET* 3.5 19.4 + - + +
1153F ASP* 4.2 6.6 - - - +
1154F PHE* 4.2 7.2 - - + +
1155F GLY* 3.5 37.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1051 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6F 741 4.7 6.1 - - - -
1047F PHE* 3.1 26.1 + - + +
1048F LEU* 3.7 11.0 - - + +
1050F GLU* 1.3 79.2 - - - +
1052F SER* 1.3 60.4 + - - +
1053F VAL 3.2 0.2 - - - -
1054F MET* 3.4 15.7 - - - +
1055F LYS* 3.3 19.2 + - - +
1065F LEU* 3.4 23.8 - - + +
1077F VAL* 5.2 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER1052 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
987F TYR 5.2 6.5 + - - -
1048F LEU 2.9 16.3 + - - -
1049F ASN* 2.9 24.6 - - - -
1050F GLU 2.8 1.2 + - - -
1051F ALA* 1.3 78.1 - - - +
1053F VAL* 1.3 57.8 + - - +
1055F LYS* 3.4 18.8 - - - +
1056F GLU* 4.4 1.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1053 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1049F ASN 3.7 13.0 - - - +
1050F GLU* 2.8 9.3 + - - +
1052F SER* 1.3 80.3 - - - +
1054F MET* 1.3 66.9 + - - +
1055F LYS 3.1 1.3 - - - -
1056F GLU* 3.0 21.3 + - + +
1057F PHE* 3.8 17.1 + - + -
1131F PHE* 3.7 35.7 - - + -
1154F PHE* 6.2 2.9 - - + -
1157F THR* 6.0 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET1054 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6F 741 3.6 26.7 - - + -
1050F GLU* 3.5 15.0 + - + +
1051F ALA* 3.4 24.2 - - - +
1053F VAL* 1.3 74.7 - - - +
1055F LYS* 1.3 66.3 + - - +
1057F PHE* 2.7 36.4 + - - +
1062F VAL* 6.0 0.2 - - - -
1063F VAL 4.6 4.5 - - - +
1064F ARG* 5.4 1.6 - - - +
1065F LEU* 3.9 19.5 + - + +
1079F MET* 4.4 17.0 - - + -
1152F GLY 3.9 12.6 - - - +
1153F ASP* 4.9 0.4 - - - -
1154F PHE* 3.5 49.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1055 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
992F TRP* 3.1 55.1 - - + +
1051F ALA 3.3 8.0 + - - +
1052F SER* 3.4 19.5 - - - +
1054F MET* 1.3 78.2 - - - +
1056F GLU* 1.3 62.3 + - - +
1057F PHE 3.4 5.7 + - - +
1058F ASN* 5.6 1.0 - - - +
1064F ARG* 5.8 1.3 - - - +
1065F LEU* 4.7 3.8 - - + +
----------------------------------------------------------
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