Contacts of the helix formed by residues 1028 - 1050 (chain F) in PDB entry 6X34
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 ASP1028 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1020F ARG* 4.6 15.9 - - + -
1025F ARG 5.2 0.2 + - - -
1026F LEU* 4.6 4.4 - - - -
1027F LEU* 1.3 77.4 - - - +
1029F GLU* 1.3 61.6 + - - +
1030F ALA* 4.7 1.3 - - + +
1031F THR* 3.7 25.0 - - - +
1032F LYS* 3.2 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1029 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1026F LEU 4.8 2.4 + - - +
1027F LEU 4.0 2.4 + - - -
1028F ASP* 1.3 70.5 - - - +
1030F ALA* 1.3 62.0 + - - +
1032F LYS* 3.4 5.9 + - - +
1033F ARG* 2.9 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1030 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1028F ASP* 3.5 0.8 - - + -
1029F GLU* 1.3 79.4 - - - +
1031F THR* 1.3 58.1 + - - +
1033F ARG* 3.3 6.2 + - - +
1034F SER* 2.9 29.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR1031 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
993F HIS* 4.9 10.3 + - - -
1028F ASP* 3.7 23.8 + - - +
1029F GLU 3.3 0.2 - - - -
1030F ALA* 1.3 78.1 - - - +
1032F LYS* 1.3 58.6 + - - +
1034F SER* 3.3 6.7 + - - -
1035F ASN* 2.9 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1032 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1026F LEU* 5.9 5.8 - - - -
1028F ASP 3.2 18.5 + - - +
1029F GLU* 3.7 7.0 - - - +
1031F THR* 1.3 79.3 - - - +
1033F ARG* 1.3 57.0 + - - +
1035F ASN* 3.3 5.5 + - - +
1036F ARG* 2.9 30.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1033 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1029F GLU 2.9 17.6 + - - +
1030F ALA* 3.3 6.7 + - - +
1032F LYS* 1.3 74.8 - - - +
1034F SER* 1.3 58.8 + - - +
1036F ARG* 3.3 6.1 + - - +
1037F ASP* 2.9 31.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1034 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1030F ALA 2.9 17.0 + - - -
1031F THR* 3.7 7.6 - - - -
1033F ARG* 1.3 77.0 - - - +
1035F ASN* 1.3 57.7 + - - +
1037F ASP* 4.7 3.1 - - - -
1038F SER* 2.9 39.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1035 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
985F VAL 4.6 0.9 - - - +
989F ALA* 3.5 19.0 - - + +
993F HIS* 3.5 31.9 - - + +
1031F THR 2.9 17.6 + - - +
1032F LYS* 3.3 6.7 + - - +
1034F SER* 1.3 77.4 - - - +
1036F ARG* 1.3 56.9 + - - +
1039F LEU* 3.2 29.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1036 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
982F THR* 5.6 2.1 - - - +
985F VAL* 4.8 2.3 - - - +
986F ASP* 5.0 19.7 - - + +
1032F LYS 2.9 17.3 + - - +
1033F ARG* 3.8 6.1 - - - +
1034F SER 3.2 0.2 - - - -
1035F ASN* 1.3 79.2 - - - +
1037F ASP* 1.3 56.9 + - - +
1040F CYS* 3.3 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1037 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1033F ARG 2.9 16.8 + - - +
1034F SER* 4.1 2.9 - - - +
1036F ARG* 1.3 78.9 - - - +
1038F SER* 1.3 60.3 + - - +
1039F LEU 3.4 0.2 - - - -
1040F CYS* 3.3 3.4 + - - +
1041F GLN* 2.9 30.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1038 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1034F SER* 2.9 20.5 + - - -
1037F ASP* 1.3 75.0 - - - +
1039F LEU* 1.3 58.3 + - - +
1041F GLN* 3.3 7.1 + - - +
1042F ALA* 2.9 29.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1039 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
928F THR* 5.8 0.7 - - - +
985F VAL* 4.7 8.3 - - + +
988F LEU* 6.3 1.3 - - + -
989F ALA* 4.7 11.0 - - + +
1034F SER 4.1 0.4 + - - -
1035F ASN* 3.2 25.3 + - - +
1037F ASP 3.4 0.4 - - - -
1038F SER* 1.3 77.8 - - - +
1040F CYS* 1.3 57.9 + - - +
1042F ALA* 3.3 6.0 + - - +
1043F VAL* 2.9 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS1040 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
981F GLN 5.4 0.7 - - - +
982F THR* 5.3 8.1 - - - -
985F VAL* 3.7 22.3 - - + +
1036F ARG 3.3 22.2 + - - +
1037F ASP* 3.3 4.9 + - - +
1038F SER 3.3 0.6 - - - -
1039F LEU* 1.3 78.4 - - - +
1041F GLN* 1.3 57.4 + - - +
1043F VAL* 3.3 4.3 + - - +
1044F ARG* 2.9 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1041 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1037F ASP 2.9 18.0 + - - +
1038F SER* 3.7 7.2 - - - +
1040F CYS* 1.3 76.6 - - - +
1042F ALA* 1.3 56.0 + - - +
1044F ARG* 3.3 6.5 + - - +
1045F THR* 2.9 30.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1042 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
874F LEU* 5.4 3.9 - - + +
877F ASN* 5.7 5.4 - - + +
878F ILE* 6.0 8.7 - - + +
928F THR* 4.9 12.9 - - + +
1038F SER 2.9 16.9 + - - +
1039F LEU* 3.7 7.0 - - - +
1041F GLN* 1.3 76.0 - - - +
1043F VAL* 1.3 58.9 + - - +
1045F THR* 3.3 6.8 + - - -
1046F LEU* 2.9 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1043 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
928F THR* 4.6 12.5 - - + +
932F LEU* 6.0 5.6 - - + -
985F VAL* 5.4 6.5 - - + -
1039F LEU 2.9 17.8 + - - +
1040F CYS* 3.7 6.7 - - - +
1042F ALA* 1.3 76.2 - - - +
1044F ARG* 1.3 58.3 + - - +
1046F LEU* 3.3 5.6 + - - +
1047F LEU* 2.9 31.3 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
1040F CYS 2.9 16.4 + - - +
1041F GLN* 3.7 7.2 - - - +
1042F ALA 3.3 0.2 - - - -
1043F VAL* 1.3 78.8 - - - +
1045F THR* 1.3 56.2 + - - +
1047F LEU* 3.8 4.9 - - - +
1048F GLY* 2.9 27.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR1045 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
877F ASN* 4.2 15.0 - - - -
969F PRO* 4.9 7.2 - - - -
971F ASP* 3.4 28.9 - - - +
1041F GLN 2.9 17.8 + - - -
1042F ALA* 3.8 5.8 - - - -
1043F VAL 3.3 0.2 - - - -
1044F ARG* 1.3 76.5 - - - +
1046F LEU* 1.3 61.2 + - - +
1049F TYR* 3.2 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1046 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
870F ILE* 4.3 18.0 - - + +
874F LEU* 3.7 32.7 - - + +
928F THR* 4.8 7.4 - - + -
1042F ALA 2.9 17.0 + - - +
1043F VAL* 3.8 6.3 - - - +
1045F THR* 1.3 77.3 - - - +
1047F LEU* 1.3 63.3 + - - +
1049F TYR* 4.2 3.0 - - - +
1050F GLY 3.7 14.4 + - - -
1051F TYR 4.2 4.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1047 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
946F ALA* 5.7 0.3 - - - +
1043F VAL 2.9 18.1 + - - +
1044F ARG* 3.9 5.8 - - - +
1046F LEU* 1.3 78.9 - - - +
1048F GLY* 1.3 60.8 + - - +
1049F TYR 3.5 0.3 + - - -
1050F GLY 4.0 3.3 - - - +
1051F TYR 3.5 12.5 - - - +
1052F ASN* 3.3 25.1 + - + +
1053F ILE* 4.3 25.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1048 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
946F ALA* 3.3 25.5 - - - +
971F ASP 3.9 8.3 - - - +
1044F ARG 2.9 15.9 + - - -
1045F THR 4.2 0.7 - - - -
1047F LEU* 1.3 75.4 - - - +
1049F TYR* 1.3 63.4 + - - +
1052F ASN* 5.8 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1049 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
873F LYS* 3.7 27.8 - - + -
946F ALA 3.4 14.6 - - - +
947F GLU* 3.6 16.0 + - - +
971F ASP* 3.4 20.6 + - + +
1045F THR 3.2 20.9 + - - +
1046F LEU 4.2 2.5 - - - +
1047F LEU 3.3 0.6 - - - -
1048F GLY* 1.3 80.1 - - - +
1050F GLY* 1.3 61.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1050 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
869F ARG* 5.4 4.0 - - - -
870F ILE* 4.8 12.0 - - - +
873F LYS* 5.2 0.8 - - - +
941F MET* 4.6 8.6 - - - +
942F ALA 5.0 0.5 + - - -
946F ALA* 4.1 13.9 - - - +
947F GLU* 5.9 1.1 - - - -
1046F LEU 3.7 7.6 + - - -
1047F LEU 4.0 2.4 - - - +
1049F TYR* 1.3 82.7 - - - +
1051F TYR* 1.3 62.6 + - - -
1052F ASN* 3.6 2.9 + - - +
----------------------------------------------------------
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