Contacts of the helix formed by residues 92 - 106 (chain G) in PDB entry 6CAJ
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 ILE 92 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91G LYS* 1.3 77.2 - - - +
93G MET* 1.3 58.2 + - - +
94G ILE 3.3 1.8 - - - -
95G GLU* 3.6 9.3 + - + +
96G ARG* 2.9 30.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 93 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31G LEU* 4.7 1.4 - - - +
34G LEU* 5.2 15.0 - - + +
46G ARG* 6.3 0.9 - - - -
47G ALA* 4.7 27.1 - - + -
50G THR* 6.2 2.5 - - - -
72G PHE* 5.1 8.6 - - + -
76G ILE* 3.4 52.3 - - + +
77G SER* 5.5 0.2 - - - -
91G LYS* 3.3 4.2 - - - +
92G ILE* 1.3 76.6 - - - +
94G ILE* 1.3 60.3 + - - +
96G ARG* 3.5 5.8 - - - +
97G GLY* 2.9 25.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 94 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31G LEU* 3.6 20.4 - - + +
34G LEU* 5.1 15.2 - - + +
35G LYS* 6.1 2.9 - - + -
91G LYS 4.2 7.6 + - - +
92G ILE 3.3 0.4 - - - -
93G MET* 1.3 79.6 - - - +
95G GLU* 1.3 56.9 + - - +
97G GLY 3.4 1.2 + - - -
98G GLU* 2.9 27.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 95 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91G LYS 4.9 1.5 + - - +
92G ILE* 3.6 12.7 + - + +
93G MET 3.4 0.4 - - - -
94G ILE* 1.3 75.6 - - - +
96G ARG* 1.3 60.8 + - - +
98G GLU* 3.4 8.6 - - - +
99G LEU* 3.0 32.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 96 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75G PHE* 4.5 18.2 - - + +
76G ILE* 5.6 0.9 - - - -
92G ILE 2.9 20.6 + - - +
93G MET* 3.5 9.9 - - + +
95G GLU* 1.3 76.3 - - - +
97G GLY* 1.3 57.2 + - - +
99G LEU* 3.3 14.8 - - + +
100G PHE* 2.9 29.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 97 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31G LEU* 4.2 11.0 - - - -
72G PHE* 3.6 28.6 - - - -
93G MET 2.9 14.8 + - - -
94G ILE 3.7 2.0 - - - -
96G ARG* 1.3 75.7 - - - +
98G GLU* 1.3 56.9 + - - +
100G PHE* 3.7 3.7 - - - +
101G LEU* 2.9 36.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 98 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31G LEU* 4.4 12.1 - - + +
94G ILE 2.9 17.7 + - - +
95G GLU* 3.4 11.7 - - - +
96G ARG 3.2 0.2 - - - -
97G GLY* 1.3 78.5 - - - +
99G LEU* 1.3 58.4 + - - +
101G LEU* 3.4 3.5 + - - +
102G ARG* 2.9 25.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 99 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95G GLU 3.0 22.0 + - - +
96G ARG* 3.3 30.1 - - + +
98G GLU* 1.3 74.9 - - - +
100G PHE* 1.3 60.7 + - - +
102G ARG* 3.4 10.0 - - + +
103G ARG* 2.9 40.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 100 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27G ILE* 3.7 43.5 - - + -
71G LEU* 4.6 23.6 - - + -
72G PHE* 4.2 15.5 - + + -
75G PHE* 4.9 16.4 - - + -
96G ARG 2.9 20.0 + - - +
97G GLY* 3.7 5.8 - - - +
99G LEU* 1.3 78.9 - - + +
101G LEU* 1.3 59.3 + - - +
103G ARG* 3.2 10.1 + - + +
104G ILE* 2.9 53.8 + - + +
233G PHE* 5.1 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 101 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24G VAL* 4.1 15.9 - - + +
27G ILE* 3.7 37.2 - - + +
28G ARG* 3.7 43.3 - - + +
31G LEU* 3.7 29.6 - - + -
97G GLY 2.9 14.9 + - - +
98G GLU* 3.8 3.8 - - - +
100G PHE* 1.3 73.3 - - + +
102G ARG* 1.3 60.4 + - - +
104G ILE* 3.8 9.9 - - + +
105G SER* 2.9 36.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 102 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98G GLU 2.9 14.9 + - - +
99G LEU* 3.4 15.3 - - + +
100G PHE 3.2 0.2 - - - -
101G LEU* 1.3 76.6 - - - +
103G ARG* 1.3 59.1 + - + +
105G SER* 3.8 3.8 - - - -
106G LEU* 2.9 40.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 103 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99G LEU* 2.9 29.6 + - + +
100G PHE* 3.2 10.1 + - + +
102G ARG* 1.3 76.2 - - + +
104G ILE* 1.3 62.6 + - + +
106G LEU* 3.4 5.4 + - - -
107G SER* 2.9 29.5 + - - -
287G ASP* 4.7 19.4 + - - +
288G LEU* 4.7 17.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 104 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24G VAL* 3.8 34.4 - - + +
27G ILE* 5.3 4.5 - - + -
100G PHE* 2.9 46.8 + - + +
101G LEU* 3.9 11.7 - - + +
103G ARG* 1.3 77.7 - - + +
105G SER* 1.3 61.4 + - - +
107G SER* 3.4 18.6 - - - -
108G ARG* 4.5 7.4 + - - +
232G SER* 4.4 12.6 - - - +
233G PHE* 3.7 45.4 - - + -
287G ASP* 5.7 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 105 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24G VAL* 4.9 12.2 - - - +
28G ARG* 5.6 3.5 + - - -
101G LEU* 2.9 24.8 + - - +
102G ARG* 3.8 5.8 - - - -
104G ILE* 1.3 76.3 - - - +
106G LEU* 1.3 68.0 + - - +
107G SER 3.2 0.9 + - - -
108G ARG* 4.2 11.1 + - - +
109G ASN* 4.6 5.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 106 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102G ARG* 2.9 27.7 + - + +
103G ARG* 3.6 6.7 - - - +
105G SER* 1.3 81.8 - - - +
107G SER* 1.3 63.3 + - - +
108G ARG 3.4 1.7 + - - -
109G ASN* 3.9 22.4 + - + +
110G LYS* 3.9 14.0 + - - +
----------------------------------------------------------
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