Contacts of the helix formed by residues 84 - 97 (chain G) in PDB entry 3JCK
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 ASP 84 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71G MET* 3.9 11.3 - - + +
72G PRO* 5.2 6.9 - - + +
81G GLU 4.7 1.3 - - - +
82G ALA 3.2 7.9 + - - +
83G VAL* 1.3 75.2 - - - +
85G ASP* 1.3 68.1 + - - +
86G VAL* 3.3 10.0 + - - +
87G PHE* 3.5 28.4 + - + +
88G GLN* 2.7 37.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 85 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83G VAL* 3.9 4.4 + - - +
84G ASP* 1.3 79.6 - - - +
86G VAL* 1.3 97.1 + - - +
88G GLN* 2.9 19.2 + - - -
89G ALA* 2.9 18.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 86 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84G ASP* 3.3 8.9 + - - +
85G ASP* 1.3 99.7 + - - +
87G PHE* 1.3 66.8 + - - +
89G ALA* 4.3 1.2 - - - +
90G LYS* 2.8 34.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 87 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79E MET* 3.3 41.8 - - + +
82E LYS* 4.8 11.0 - - + -
83E ILE* 4.0 6.1 - - + -
69G PHE* 3.8 20.0 - + - -
70G ALA 3.2 28.7 - - - -
71G MET* 3.5 18.2 - - - -
72G PRO* 3.8 25.4 - - + -
84G ASP* 3.4 27.5 + - + +
85G ASP 3.3 0.4 - - - -
86G VAL* 1.3 81.3 - - - +
88G GLN* 1.3 68.3 + - - +
90G LYS* 3.3 5.9 + - - +
91G MET* 2.9 27.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 88 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52G LEU* 3.7 19.9 - - + +
69G PHE* 4.2 10.3 - - + -
71G MET* 5.1 1.6 - - + -
83G VAL* 3.9 19.9 - - - +
84G ASP 2.7 20.4 + - - +
85G ASP* 2.9 10.2 + - - +
87G PHE* 1.3 77.6 - - - +
89G ALA* 1.3 56.3 + - - +
91G MET* 2.7 26.3 + - - +
92G MET* 2.8 23.0 + - + +
104G VAL* 3.6 29.3 - - - +
132G LEU* 6.2 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 89 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85G ASP 2.9 12.5 + - - +
86G VAL* 4.5 1.3 - - - +
88G GLN* 1.3 77.0 - - - +
90G LYS* 1.3 59.5 + - - +
92G MET* 2.8 30.5 + - + +
93G ASP* 2.9 17.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 90 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75E ASN* 4.6 17.4 + - - -
78E GLU* 4.5 13.5 + - - -
79E MET* 3.7 17.7 - - - +
86G VAL* 2.8 29.4 + - + +
87G PHE* 3.3 7.0 - - - +
89G ALA* 1.3 75.0 - - - +
91G MET* 1.3 56.7 + - - +
93G ASP* 2.6 24.3 - - - +
94G MET* 3.2 33.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 91 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76E MET* 4.4 15.3 - - - +
79E MET* 3.6 30.0 - - + +
80E CYS* 6.5 0.7 - - - -
83E ILE* 6.4 0.2 - - + -
69G PHE* 3.7 49.8 - - + -
70G ALA 5.3 1.1 - - - +
87G PHE* 2.9 24.7 + - + +
88G GLN 2.7 15.4 + - - +
90G LYS* 1.3 71.9 - - - +
92G MET* 1.3 68.0 + - - +
94G MET* 3.2 3.6 + - - +
95G LEU* 2.9 41.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 92 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54G LEU* 4.3 17.9 - - + -
69G PHE* 3.4 39.0 - - + -
88G GLN* 2.8 25.2 + - + +
89G ALA* 2.8 23.1 + - + +
91G MET* 1.3 73.4 - - + +
93G ASP* 1.3 55.9 + - - +
95G LEU* 2.7 30.3 + - + +
96G LYS* 2.8 37.8 + - - +
102G GLN 5.1 7.4 - - - +
104G VAL* 4.7 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 93 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89G ALA 2.9 9.3 + - - +
90G LYS* 2.6 29.6 - - - +
92G MET* 1.3 76.0 - - - +
94G MET* 1.3 82.1 + - - +
96G LYS* 2.8 36.6 + - + +
97G GLN* 3.0 17.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 94 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72E TYR* 2.7 72.7 + - + +
75E ASN* 3.8 10.3 - - + +
76E MET* 3.5 29.4 - - + +
79E MET* 3.8 14.6 - - - -
90G LYS* 3.2 40.4 - - - +
91G MET* 3.7 4.0 - - - +
92G MET 3.2 1.0 - - - -
93G ASP* 1.3 89.8 + - - +
95G LEU* 1.3 59.9 + - - +
97G GLN* 3.9 14.1 + - - +
98G THR* 3.7 5.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 95 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72E TYR* 5.2 1.8 - - - +
76E MET* 5.2 4.7 - - + -
54G LEU* 4.1 26.0 - - + -
67G ASP* 5.9 1.1 - - + +
68G VAL 6.1 0.4 - - - +
69G PHE* 4.8 4.0 - - + -
91G MET* 2.9 43.7 + - + +
92G MET* 2.7 13.3 + - + +
94G MET* 1.3 77.5 - - - +
96G LYS* 1.3 57.0 + - + +
97G GLN 3.1 1.3 - - - -
98G THR* 2.3 44.5 + - + +
99G GLY 2.9 6.2 + - - -
100G ARG* 3.2 33.0 + - + +
101G ASP* 4.1 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 96 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92G MET* 2.8 58.4 + - - +
93G ASP* 2.8 22.8 + - + +
95G LEU* 1.3 70.5 - - + +
97G GLN* 1.3 54.9 + - + +
99G GLY* 2.7 23.9 + - - -
101G ASP* 2.9 40.3 + - - +
102G GLN 5.5 3.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 97 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55E PRO* 4.0 25.2 - - + +
69E ASP* 5.8 2.3 + - - -
72E TYR* 3.0 34.8 - - - -
93G ASP* 3.0 17.9 + - - +
94G MET* 3.9 10.0 - - - +
95G LEU 3.1 0.4 - - - -
96G LYS* 1.3 76.5 - - + +
98G THR* 1.3 59.3 + - - +
----------------------------------------------------------
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