Contacts of the helix formed by residues 1053 - 1058 (chain O) in PDB entry 5X0X
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 MET1053 (chain O).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1026O MET* 3.3 55.3 - - + +
1029O TYR* 3.3 32.1 - - + +
1030O ARG* 3.3 12.8 - - + +
1046O ARG* 3.5 43.1 - - - +
1047O GLY 4.9 0.4 - - - -
1048O PHE 3.0 26.2 + - - +
1049O ASN* 3.1 24.0 - - - +
1052O ILE* 1.3 78.8 - - - +
1054O GLN* 1.3 69.7 + - - +
1056O LYS* 4.4 0.3 - - - +
1057O LYS* 3.4 4.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1054 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1026O MET* 5.9 0.6 - - - +
1027O LEU* 5.5 4.4 - - - +
1030O ARG* 5.3 7.1 - - - +
1049O ASN* 2.5 43.6 + - + +
1050O ASN* 3.2 22.2 - - - +
1051O GLN 3.4 0.2 + - - -
1053O MET* 1.3 74.6 - - - +
1055O LEU* 1.3 60.7 + - + +
1056O LYS 3.0 4.0 - - - -
1057O LYS* 2.5 66.5 + - - +
1058O ILE* 3.8 4.9 - - - +
1217O VAL* 3.5 32.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1055 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1050O ASN* 3.1 15.5 - - - +
1051O GLN* 2.9 45.5 + - - +
1054O GLN* 1.3 73.6 - - + +
1056O LYS* 1.3 62.2 + - - +
1058O ILE* 3.2 22.8 + - + -
1060O ASN* 2.7 40.0 + - - +
1061O HIS* 4.8 0.4 - - - -
1112O MET* 3.6 23.8 - - + -
1182O ASP* 6.4 0.4 - - + -
1183O THR* 3.5 33.2 - - + +
1185O TRP* 5.4 1.8 - - - +
1217O VAL* 5.7 0.2 - - + -
1221O ILE* 4.7 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1056 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11J T 2.8 31.2 + - - -
1019O GLN* 4.5 5.0 + - - +
1023O TYR* 5.9 4.5 - - + -
1026O MET* 5.6 3.4 - - + -
1051O GLN 3.4 7.7 + - - +
1052O ILE* 3.4 43.8 - - - +
1053O MET 4.4 2.5 - - - +
1054O GLN 2.8 1.2 + - - +
1055O LEU* 1.3 79.0 - - - +
1057O LYS* 1.3 61.9 + - + +
1058O ILE 3.1 1.2 + - - -
1059O CYS 3.8 2.8 + - - -
1061O HIS* 3.5 62.3 + - + +
1064O VAL* 3.6 26.5 - - + -
1065O PHE* 5.0 5.2 - - + -
1112O MET* 4.2 9.3 - - - -
1114O GLN* 5.9 1.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1057 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1015O MET* 3.1 27.1 - - + +
1019O GLN* 3.8 14.0 - - - +
1023O TYR* 3.1 40.0 + - + +
1024O GLN* 4.8 6.5 + - - +
1026O MET* 3.5 33.7 - - - +
1027O LEU* 4.9 9.7 - - - +
1053O MET 3.4 11.7 - - - +
1054O GLN* 2.5 52.5 + - - +
1056O LYS* 1.3 73.2 - - - +
1058O ILE* 1.3 57.7 + - + +
1059O CYS 3.0 7.9 + - - -
1217O VAL* 4.7 7.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1058 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1015O MET* 4.4 7.9 - - + -
1054O GLN 3.8 5.6 - - - +
1055O LEU* 3.2 36.5 + - + -
1056O LYS 3.1 3.0 + - - -
1057O LYS* 1.3 77.0 - - + +
1059O CYS* 1.3 69.7 + - - +
1060O ASN* 3.0 29.8 + - - +
1088O LYS* 5.4 0.9 - - - +
1182O ASP* 5.0 1.8 - - - +
1183O THR* 4.9 0.7 - - + -
1213O THR* 4.2 8.2 - - - +
1216O SER* 5.1 2.2 - - - -
1217O VAL* 3.6 31.6 - - + +
1218O GLU* 3.5 48.7 - - + +
1221O ILE* 6.1 0.2 - - + -
----------------------------------------------------------
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