Contacts of the helix formed by residues 1023 - 1036 (chain A) in PDB entry 4X7J
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 THR1023 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1021A PHE* 4.0 4.7 - - - +
1022A SER* 1.3 87.5 - - - +
1024A GLN* 1.3 63.6 + - - +
1025A MET* 3.8 9.3 + - - +
1026A GLU* 3.2 27.0 + - - +
1027A ARG* 3.1 21.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1024 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
897A LYS* 4.8 9.8 + - - +
901A ASN* 5.2 10.3 + - - +
1023A THR* 1.3 72.5 - - - +
1025A MET* 1.3 61.8 + - - +
1027A ARG* 2.7 44.8 + - - +
1028A VAL* 3.1 34.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET1025 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1023A THR* 3.2 8.6 - - - +
1024A GLN* 1.3 78.8 - - - +
1026A GLU* 1.3 61.1 + - - +
1028A VAL* 3.6 4.9 + - - +
1029A ARG* 3.2 24.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1026 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1019A TYR* 4.2 11.3 + - - -
1020A PRO 4.1 7.8 - - - +
1021A PHE* 3.6 22.1 - - + -
1022A SER* 3.0 33.1 + - - -
1023A THR* 3.2 20.3 + - - +
1025A MET* 1.3 72.7 - - - +
1027A ARG* 1.3 57.9 + - - +
1029A ARG* 3.5 4.2 + - - +
1030A THR* 2.7 43.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1027 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
897A LYS* 3.9 23.9 - - - +
901A ASN* 5.4 7.2 - - - -
989A LEU* 4.0 17.6 - - - +
990A TYR* 2.8 34.9 + - - -
1016A GLU* 2.9 19.2 + - - -
1021A PHE* 3.6 39.2 - - + -
1023A THR 3.1 11.2 + - - +
1024A GLN* 2.7 49.3 + - - +
1026A GLU* 1.3 76.8 - - - +
1028A VAL* 1.3 59.9 + - - +
1030A THR* 3.9 0.5 - - - -
1031A LEU* 3.0 43.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1028 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
989A LEU* 4.3 21.5 - - + +
1024A GLN* 3.1 34.7 + - + +
1025A MET* 4.1 5.4 - - - +
1026A GLU 3.4 0.2 - - - -
1027A ARG* 1.3 80.8 - - - +
1029A ARG* 1.3 60.8 + - - +
1031A LEU* 4.0 0.5 - - - +
1032A THR* 2.8 41.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1029 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1025A MET* 3.2 16.9 + - + +
1026A GLU* 3.8 6.3 - - - +
1028A VAL* 1.3 80.0 - - - +
1030A THR* 1.3 57.8 + - - +
1032A THR* 3.7 4.9 - - - -
1033A ASP* 3.1 42.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR1030 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1015A PHE* 3.8 17.9 - - + -
1019A TYR* 4.3 4.4 - - + +
1021A PHE* 3.6 21.0 - - + -
1026A GLU* 2.7 29.4 + - - +
1029A ARG* 1.3 75.6 - - - +
1031A LEU* 1.3 59.6 + - - +
1033A ASP* 3.2 9.3 + - + +
1034A VAL* 2.9 32.1 + - - +
1040A PRO* 3.7 31.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1031 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
989A LEU* 4.0 22.4 - - + -
990A TYR* 3.8 29.2 - - + +
1012A LEU* 3.7 20.5 - - + +
1015A PHE* 3.8 30.5 - - + -
1016A GLU* 4.0 20.4 - - + +
1021A PHE* 4.2 11.2 - - + -
1027A ARG* 3.0 32.0 + - + +
1028A VAL 4.2 1.8 - - - +
1030A THR* 1.3 72.9 - - - +
1032A THR* 1.3 61.6 + - - +
1034A VAL* 4.2 2.2 - - - -
1035A ARG* 2.9 34.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR1032 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
989A LEU* 3.5 16.0 - - - +
1028A VAL* 2.8 28.4 + - - +
1029A ARG* 3.7 5.8 - - - -
1031A LEU* 1.3 77.2 - - - +
1033A ASP* 1.3 65.0 + - - +
1035A ARG* 3.3 21.9 - - - +
1036A ASN* 3.2 26.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1033 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1029A ARG* 3.1 27.9 + - - +
1030A THR* 3.2 12.8 + - + +
1032A THR* 1.3 77.9 - - - +
1034A VAL* 1.3 58.9 + - - +
1036A ASN* 2.9 18.7 + - - +
1037A LEU 3.1 0.2 + - - -
1038A LYS* 2.9 46.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1034 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1012A LEU* 4.1 11.2 - - + -
1015A PHE* 3.7 47.6 - - + -
1030A THR 2.9 20.3 + - - +
1031A LEU* 3.7 7.0 - - - +
1033A ASP* 1.3 71.8 - - - +
1035A ARG* 1.3 61.7 + - - +
1037A LEU* 2.9 20.8 + - - +
1038A LYS 3.7 13.7 - - - +
1039A PHE* 3.8 19.9 - - + -
1040A PRO* 4.3 4.3 - - + -
1058A LEU* 3.5 28.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1035 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
988A LYS 4.1 2.0 + - - -
989A LEU* 2.8 47.8 + - - +
991A MET 2.9 30.3 + - - +
993A PRO* 4.1 14.8 - - - +
996A ILE* 3.4 20.2 - - - +
1008A PHE* 3.5 34.4 - - + -
1012A LEU* 3.9 17.7 - - + +
1031A LEU 2.9 21.9 + - - +
1032A THR* 3.3 20.2 - - - +
1034A VAL* 1.3 77.0 - - - +
1036A ASN* 1.3 63.6 + - - +
1037A LEU* 3.3 6.1 + - - +
1058A LEU* 4.8 9.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1036 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1032A THR* 3.2 22.6 - - - +
1033A ASP* 2.9 11.7 + - - +
1035A ARG* 1.3 83.3 + - - +
1037A LEU* 1.3 71.9 + - - +
1038A LYS* 3.3 5.9 + - + +
----------------------------------------------------------
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