Contacts of the helix formed by residues 62 - 83 (chain G) in PDB entry 6O81
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 SER 62 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22G SER* 4.5 13.1 + - - -
57G CYS* 6.0 0.3 - - - +
60G ASP* 3.2 7.3 - - - +
61G SER* 1.3 80.5 + - - +
63G VAL* 1.3 62.7 + - - +
64G ALA* 3.3 9.6 - - - -
65G VAL* 3.4 23.8 - - - +
66G SER* 4.0 1.6 + - - -
198G GLU* 4.9 12.0 + - - -
250G PHE* 3.4 13.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 63 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61G SER 4.1 0.2 + - - -
62G SER* 1.3 72.6 - - - +
64G ALA* 1.3 61.5 + - - +
65G VAL 3.4 0.4 - - - -
66G SER* 3.3 1.6 + - - -
67G SER* 2.9 28.9 + - - -
198G GLU* 3.4 34.5 - - + +
199G GLY* 3.9 3.4 - - - -
207G ILE* 3.7 41.3 - - + -
236G VAL* 4.4 22.0 - - + -
238G LEU* 5.5 0.2 - - + -
250G PHE* 3.7 36.1 - - + +
273G VAL* 5.8 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 64 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22G SER* 4.4 9.6 - - - +
23G ALA* 3.4 25.9 - - + +
62G SER* 3.3 5.2 - - - -
63G VAL* 1.3 81.0 - - - +
65G VAL* 1.3 57.2 + - - +
67G SER* 2.9 19.8 + - - -
68G GLY 2.9 13.0 + - - -
198G GLU* 3.6 22.9 - - + +
233G PHE 4.0 0.7 - - - +
234G LYS* 4.6 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 65 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10G PHE* 4.2 9.9 - - + -
22G SER* 3.3 44.6 - - - +
23G ALA* 4.4 4.0 - - - +
26G ALA* 3.8 19.0 - - + +
53G ILE* 5.4 1.4 - - - +
56G LEU* 4.7 11.4 - - + +
57G CYS* 5.1 4.0 - - - -
60G ASP* 3.8 27.8 - - + +
62G SER* 3.4 21.1 - - - +
64G ALA* 1.3 77.5 - - - +
66G SER* 1.3 60.6 + - - +
68G GLY* 3.8 0.4 - - - -
69G GLY* 2.9 25.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 66 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53G ILE* 5.1 10.3 - - - +
57G CYS* 5.2 12.3 - - - -
62G SER 4.3 1.3 - - - -
63G VAL 3.3 7.9 + - - -
64G ALA 3.3 0.4 - - - -
65G VAL* 1.3 80.8 - - - +
67G SER* 1.3 59.7 + - - +
69G GLY* 3.4 1.9 + - - -
70G GLU* 2.9 28.3 + - - +
236G VAL* 5.1 6.2 - - - +
249G LYS* 5.4 2.6 - - - -
250G PHE* 3.7 31.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 67 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63G VAL* 2.9 16.4 + - - -
64G ALA* 2.9 20.4 + - - -
66G SER* 1.3 76.3 + - - +
68G GLY* 1.3 55.4 + - - +
70G GLU* 3.3 6.4 + - - +
71G LEU* 2.9 33.1 + - - +
198G GLU 5.0 0.2 + - - -
199G GLY* 5.5 0.5 - - - -
233G PHE 3.1 14.0 + - - -
234G LYS* 3.8 6.5 + - - -
235G PHE 3.4 23.5 - - - +
236G VAL* 3.8 19.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 68 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23G ALA* 5.1 2.5 - - - -
26G ALA* 6.1 1.3 - - - -
27G ILE* 4.1 27.7 - - - +
30G LEU* 5.0 0.7 - - - -
64G ALA 2.9 16.7 + - - -
65G VAL* 3.9 2.0 - - - -
67G SER* 1.3 77.0 + - - +
69G GLY* 1.3 56.5 + - - +
71G LEU* 3.8 4.7 - - - +
72G PHE* 2.9 29.6 + - - +
233G PHE* 3.6 9.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 69 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26G ALA* 5.8 0.6 - - - +
30G LEU* 3.8 22.2 - - - +
53G ILE* 3.3 28.7 - - - +
65G VAL 2.9 17.9 + - - -
66G SER 3.8 1.8 - - - -
68G GLY* 1.3 73.8 - - - +
70G GLU* 1.3 57.9 + - - +
72G PHE* 3.3 0.9 + - - +
73G LEU* 2.9 24.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 70 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53G ILE* 5.2 1.9 - - - +
66G SER 2.9 18.2 + - - +
67G SER* 3.3 7.8 + - - +
69G GLY* 1.3 76.4 - - - +
71G LEU* 1.3 60.2 + - + +
73G LEU* 3.4 8.5 + - - +
74G ARG* 2.9 28.8 + - - +
235G PHE 5.8 1.3 - - - +
236G VAL* 6.1 3.8 - - + -
237G ARG* 5.5 13.7 - - + +
305G LEU* 4.1 34.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 71 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27G ILE* 6.1 1.3 - - + -
67G SER 2.9 19.6 + - - +
68G GLY* 3.9 4.0 - - - +
70G GLU* 1.3 80.0 - - + +
72G PHE* 1.3 59.1 + - - +
74G ARG* 3.4 3.9 + - + +
75G PHE* 2.9 27.5 + - - +
100G PHE* 5.6 14.6 - - + -
232G SER* 3.4 26.2 - - - +
233G PHE* 3.8 18.2 - - + +
235G PHE* 4.1 15.5 - - + +
300G LEU* 4.9 9.6 - - + -
303G LEU* 3.7 29.9 - - + +
305G LEU 4.8 9.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 72 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27G ILE* 4.5 20.9 - - + -
30G LEU* 3.7 50.5 - - + -
31G LEU* 4.1 28.0 - - + -
34G LEU* 4.6 7.0 - - + -
49G LEU* 3.8 29.6 - - + -
53G ILE* 5.9 0.9 - - + -
68G GLY 2.9 18.7 + - - +
69G GLY 3.8 3.4 - - - +
71G LEU* 1.3 73.2 - - - +
73G LEU* 1.3 61.6 + - - +
75G PHE* 3.3 18.1 + + + +
76G ILE* 2.9 27.3 + - + +
93G MET* 5.5 11.0 - - + -
97G GLY* 5.3 6.1 - - - -
100G PHE* 5.6 9.4 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 73 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49G LEU* 5.1 8.1 - - + -
53G ILE* 4.3 13.5 - - + -
69G GLY 2.9 17.0 + - - +
70G GLU* 3.7 12.1 - - - +
72G PHE* 1.3 76.1 - - - +
74G ARG* 1.3 59.1 + - - +
76G ILE* 3.4 6.6 + - - +
77G SER* 2.9 29.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 74 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70G GLU* 2.9 18.7 + - - +
71G LEU* 3.7 7.2 - - - +
73G LEU* 1.3 76.1 - - - +
75G PHE* 1.3 58.2 + - - +
77G SER* 3.4 12.6 + - - -
78G LEU* 2.9 59.2 + - + +
303G LEU* 2.9 35.4 + - + +
304G TYR* 2.6 40.2 + - - +
305G LEU* 3.5 24.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 75 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71G LEU 2.9 18.3 + - - +
72G PHE* 3.6 19.7 - + + +
74G ARG* 1.3 77.3 - - - +
76G ILE* 1.3 56.9 + - - +
78G LEU* 3.3 19.9 + - + +
79G ALA* 2.9 29.9 + - + +
93G MET* 4.7 12.8 - - + -
96G ARG* 3.6 56.3 - - + -
97G GLY* 4.1 7.2 - - - -
100G PHE* 4.8 24.5 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 76 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46G ARG* 5.4 6.5 - - + -
49G LEU* 3.9 23.6 - - + -
72G PHE* 2.9 20.0 + - + +
73G LEU 3.8 4.3 - - - +
75G PHE* 1.3 73.8 - - - +
77G SER* 1.3 60.4 + - - +
79G ALA* 3.4 1.9 + - - +
80G SER* 2.9 29.1 + - - -
93G MET* 3.9 30.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 77 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46G ARG* 3.1 36.2 + - - +
73G LEU 2.9 17.2 + - - -
74G ARG* 3.7 16.9 + - - -
76G ILE* 1.3 77.5 - - - +
78G LEU* 1.3 56.6 + - - +
80G SER* 3.4 1.6 + - - -
81G LEU* 2.9 31.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 78 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74G ARG* 2.9 40.9 + - + +
75G PHE* 3.6 21.3 - - + +
77G SER* 1.3 77.7 - - - +
79G ALA* 1.3 58.0 + - - +
81G LEU* 3.4 4.8 + - - +
82G GLU* 2.9 34.4 + - + +
96G ARG* 4.2 17.5 - - - +
303G LEU* 5.4 12.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 79 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75G PHE* 2.9 18.9 + - + +
76G ILE 3.8 0.2 - - - +
78G LEU* 1.3 75.9 - - + +
80G SER* 1.3 60.9 + - - +
82G GLU* 4.5 0.2 - - - -
83G TYR* 3.5 29.7 + - + +
89G CYS* 4.3 6.8 - - - +
93G MET* 3.8 42.6 - - + +
96G ARG* 4.3 22.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 80 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42G ILE* 5.5 11.9 - - - -
46G ARG* 4.1 17.9 - - - -
76G ILE 2.9 18.1 + - - -
77G SER 3.8 4.0 - - - -
78G LEU 3.3 0.4 - - - -
79G ALA* 1.3 78.0 - - - +
81G LEU* 1.3 55.9 + - - +
83G TYR 3.0 20.9 - - - +
86G TYR* 5.9 8.3 - - - -
89G CYS* 5.5 3.8 - - - -
93G MET* 4.7 5.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 81 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46G ARG* 5.2 2.2 - - - +
77G SER* 2.9 19.5 + - - +
78G LEU* 4.0 5.2 - - - +
80G SER* 1.3 75.0 - - - +
82G GLU* 1.3 65.2 + - - +
83G TYR 4.6 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 82 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78G LEU* 2.9 21.1 + - + +
79G ALA 4.1 0.9 - - - +
80G SER 3.4 0.2 - - - -
81G LEU* 1.3 80.5 - - - +
83G TYR* 1.3 80.4 + - + +
84G SER 4.0 0.7 + - - -
96G ARG* 4.4 11.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 83 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79G ALA* 3.5 16.5 + - + +
80G SER* 3.0 21.5 - - - +
81G LEU 4.9 0.7 - - - -
82G GLU* 1.3 82.2 - - + +
84G SER* 1.3 65.3 + - - +
85G ASP 4.0 5.3 - - - +
88G LYS* 5.5 8.1 - - + -
89G CYS* 3.8 27.1 - - + +
92G ILE* 3.7 30.8 - - + +
96G ARG* 3.4 38.1 + - - -
----------------------------------------------------------
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