Contacts of the helix formed by residues 1065 - 1078 (chain G) in PDB entry 6BAA
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 ALA1065 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1064G TYR* 1.3 81.4 - - - +
1066G MET* 1.3 55.4 + - - +
1068G PHE* 5.0 0.9 - - - -
1069G THR* 2.8 38.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET1066 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1064G TYR 3.3 5.1 - - - +
1065G ALA* 1.3 80.2 - - - +
1067G VAL* 1.3 61.8 + - + +
1069G THR* 3.7 2.9 - - - -
1070G LEU* 2.9 25.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1067 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1033G TRP* 5.1 12.0 - - + +
1036G LYS 5.9 0.9 - - - +
1037G TRP* 5.1 19.7 - - + +
1064G TYR* 4.5 1.8 + - - +
1066G MET* 1.3 79.7 - - + +
1068G PHE* 1.3 58.8 + - - +
1070G LEU* 3.3 10.4 + - + +
1071G LEU* 2.8 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1068 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
560G VAL* 5.9 9.2 - - + -
563G VAL* 6.3 3.1 - - + -
1064G TYR 3.3 20.6 + - - +
1065G ALA* 4.3 0.9 - - - +
1067G VAL* 1.3 76.8 - - - +
1069G THR* 1.3 60.0 + - - +
1071G LEU* 3.1 8.7 + - - +
1072G CYS* 2.9 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR1069 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1065G ALA* 2.8 23.7 + - - -
1066G MET* 3.7 3.4 - - - -
1068G PHE* 1.3 75.0 - - - +
1070G LEU* 1.3 57.4 + - - +
1072G CYS* 3.4 6.5 + - - +
1073G SER* 2.9 30.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1070 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1033G TRP* 5.8 6.3 - - + -
1066G MET 2.9 13.8 + - - +
1067G VAL* 3.3 15.0 - - + +
1069G THR* 1.3 77.0 - - - +
1071G LEU* 1.3 56.5 + - - +
1073G SER* 3.4 6.9 + - - -
1074G LEU* 2.8 29.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1071 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556G LEU* 5.4 4.5 - - + +
1030G ILE* 5.7 9.7 - - + +
1033G TRP* 5.9 8.5 - - + +
1034G LEU* 6.1 3.4 - - + +
1067G VAL 2.8 16.4 + - - +
1068G PHE* 3.1 11.8 + - - +
1070G LEU* 1.3 70.6 - - - +
1072G CYS* 1.3 61.2 + - - +
1074G LEU* 3.2 8.1 + - - +
1075G GLY* 2.9 25.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS1072 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556G LEU* 5.3 10.5 - - + -
1068G PHE 2.9 15.5 + - - +
1069G THR* 3.8 7.0 - - - +
1071G LEU* 1.3 75.7 - - - +
1073G SER* 1.3 62.7 + - - +
1075G GLY* 3.1 1.9 + - - -
1076G ILE* 3.1 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1073 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1069G THR 2.9 17.9 + - - -
1070G LEU* 3.6 7.0 - - - -
1072G CYS* 1.3 76.9 - - - +
1074G LEU* 1.3 61.6 + - - +
1076G ILE* 3.8 11.5 + - - +
1077G VAL* 4.0 9.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1074 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1026G VAL* 4.8 13.0 - - + +
1029G ALA* 5.6 3.8 - - + -
1030G ILE* 4.9 20.6 - - + +
1070G LEU 2.8 16.9 + - - +
1071G LEU* 3.5 9.2 - - - +
1072G CYS 3.2 0.2 - - - -
1073G SER* 1.3 78.1 - - - +
1075G GLY* 1.3 58.2 + - - +
1077G VAL* 3.1 27.1 + - - +
1078G LEU* 4.1 2.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1075 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552G ILE* 3.3 33.3 - - - +
556G LEU* 5.5 5.8 - - - -
1030G ILE* 5.9 4.5 - - - -
1071G LEU 2.9 14.5 + - - -
1072G CYS* 3.1 4.8 + - - -
1074G LEU* 1.3 74.2 - - - +
1076G ILE* 1.3 64.4 + - - +
1078G LEU* 4.0 8.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1076 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1072G CYS 3.1 15.6 + - - +
1073G SER* 4.0 8.3 - - - +
1074G LEU 3.2 0.4 - - - -
1075G GLY* 1.3 78.3 - - - +
1077G VAL* 1.3 62.4 + - - +
1078G LEU 3.2 10.9 + - - +
1079G CYS* 5.0 2.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1077 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1023G LYS* 5.6 1.1 - - - +
1026G VAL* 4.7 12.6 - - + -
1073G SER 4.0 5.7 + - - +
1074G LEU* 3.1 18.5 + - - +
1076G ILE* 1.3 78.1 - - - +
1078G LEU* 1.3 62.5 + - - +
1079G CYS* 3.3 11.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1078 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545G PHE* 4.5 7.0 - - - -
548G THR 6.4 0.4 - - - -
549G ALA* 4.9 9.0 - - + +
552G ILE* 4.3 27.1 - - + -
1023G LYS* 4.6 23.3 - - + +
1026G VAL* 5.2 5.4 - - + +
1074G LEU 4.1 2.5 + - - +
1075G GLY* 4.0 8.3 + - - +
1076G ILE 3.2 12.6 + - - +
1077G VAL* 1.3 75.7 - - - +
1079G CYS* 1.3 59.4 + - - +
----------------------------------------------------------
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