Contacts of the helix formed by residues 45 - 71 (chain G) in PDB entry 6RI7
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 ASN 45 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C TYR* 4.0 1.9 + - - -
36G ALA* 5.6 2.7 - - + +
40G GLY* 5.3 11.0 - - - -
42G ARG* 4.0 14.4 + - + +
43G SER 3.5 2.0 - - - -
44G GLU* 1.3 75.0 - - - +
46G ALA* 1.3 61.3 + - - +
47G ASP* 3.2 3.4 - - + +
48G TYR* 3.6 25.4 - - + +
49G GLN* 2.9 27.5 + - - +
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Residues in contact with ALA 46 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C TYR* 3.5 31.2 - - + -
480C SER* 5.7 3.1 - - - +
44G GLU 3.0 6.8 + - - +
45G ASN* 1.3 69.4 - - - +
47G ASP* 1.3 66.2 + - - +
49G GLN* 3.6 2.5 - - - +
50G TYR* 2.9 26.0 + - - +
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Residues in contact with ASP 47 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36G ALA* 4.4 13.7 - - + -
45G ASN* 3.2 3.3 - - + +
46G ALA* 1.3 80.0 - - - +
48G TYR* 1.3 57.9 + - - +
50G TYR* 3.4 5.2 + - - +
51G ASN* 2.9 29.1 + - - +
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Residues in contact with TYR 48 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36G ALA* 3.9 22.3 - - + +
37G ALA 5.7 0.2 - - - +
41G ASP* 6.1 2.2 - - - +
42G ARG 4.8 8.1 - - - +
45G ASN* 3.2 25.1 + - + +
47G ASP* 1.3 78.7 - - - +
49G GLN* 1.3 58.3 + - - +
51G ASN* 3.3 4.4 + - - +
52G LYS* 2.9 31.2 + - - +
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Residues in contact with GLN 49 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C TYR* 4.1 22.4 - - + +
477C GLU* 4.7 19.1 - - - +
480C SER* 5.3 7.4 - - - +
45G ASN 2.9 13.4 + - - +
46G ALA* 3.3 8.3 + - - +
48G TYR* 1.3 76.9 - - - +
50G TYR* 1.3 63.3 + - - +
52G LYS* 3.3 4.3 + - - +
53G LYS* 3.0 25.0 + - - +
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Residues in contact with TYR 50 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46G ALA 2.9 16.1 + - - +
47G ASP* 3.8 4.5 - - - +
49G GLN* 1.3 76.5 - - - +
51G ASN* 1.3 58.9 + - - +
53G LYS* 3.4 5.6 + - - +
54G ARG* 2.9 31.2 + - - +
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Residues in contact with ASN 51 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29G VAL* 5.1 3.4 - - - +
32G LYS* 4.7 9.0 - - + +
33G VAL* 4.2 33.6 - - + +
47G ASP 2.9 17.7 + - - +
48G TYR* 3.6 8.5 - - - +
49G GLN 3.2 0.2 - - - -
50G TYR* 1.3 77.4 - - - +
52G LYS* 1.3 57.0 + - - +
54G ARG* 3.4 5.2 + - - +
55G LEU* 2.9 28.8 + - - +
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Residues in contact with LYS 52 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48G TYR 2.9 17.3 + - - +
49G GLN* 3.8 5.2 - - - +
51G ASN* 1.3 75.4 - - - +
53G LYS* 1.3 63.8 + - - +
55G LEU* 3.2 8.2 + - - +
56G ARG* 2.9 23.7 + - - +
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Residues in contact with LYS 53 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477C GLU* 4.7 12.6 - - - +
481C LEU* 6.5 1.3 - - + -
49G GLN 3.0 17.6 + - - +
50G TYR* 3.8 6.3 - - - +
52G LYS* 1.3 76.1 - - - +
54G ARG* 1.3 57.4 + - - +
56G ARG* 3.2 7.5 + - - +
57G GLU* 2.9 28.7 + - - +
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Residues in contact with ARG 54 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29G VAL* 5.8 6.5 - - + -
50G TYR 2.9 18.3 + - - +
51G ASN* 3.8 5.6 - - - +
53G LYS* 1.3 76.7 - - - +
55G LEU* 1.3 57.6 + - - +
57G GLU* 3.7 6.9 - - - +
58G ILE* 2.8 31.8 + - - +
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Residues in contact with LEU 55 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29G VAL* 5.8 6.9 - - + +
51G ASN 2.9 18.1 + - - +
52G LYS* 3.2 9.6 + - - +
54G ARG* 1.3 74.7 - - - +
56G ARG* 1.3 65.8 + - - +
58G ILE* 3.3 5.3 + - - +
59G ASP* 2.9 25.0 + - - +
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Residues in contact with ARG 56 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52G LYS 2.9 12.4 + - - +
53G LYS* 3.6 9.0 - - - +
55G LEU* 1.3 75.4 - - - +
57G GLU* 1.3 64.2 + - - +
59G ASP* 3.3 7.6 + - - +
60G ARG* 3.0 23.0 + - - +
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Residues in contact with GLU 57 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53G LYS 2.9 16.7 + - - +
54G ARG* 3.7 8.1 - - - +
56G ARG* 1.3 78.1 - - - +
58G ILE* 1.3 56.9 + - - +
60G ARG* 3.2 6.9 + - - +
61G ARG* 2.9 29.6 + - - +
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Residues in contact with ILE 58 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25G GLU* 6.5 0.7 - - + -
26G ARG* 6.0 7.9 - - + -
54G ARG 2.8 18.8 + - - +
55G LEU* 3.8 5.6 - - - +
57G GLU* 1.3 76.4 - - - +
59G ASP* 1.3 58.0 + - - +
61G ARG* 3.4 6.1 + - - +
62G VAL* 2.9 31.9 + - - +
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Residues in contact with ASP 59 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55G LEU 2.9 16.8 + - - +
56G ARG* 3.5 8.3 - - - +
58G ILE* 1.3 78.0 - - - +
60G ARG* 1.3 63.5 + - - +
62G VAL* 3.7 4.5 - - - +
63G ARG* 2.9 24.8 + - - +
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Residues in contact with ARG 60 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56G ARG 3.0 15.8 + - - +
57G GLU* 3.2 6.5 + - - +
59G ASP* 1.3 75.6 - - - +
61G ARG* 1.3 63.3 + - - +
63G ARG* 3.3 6.7 + - - +
64G TYR* 3.0 24.8 + - - +
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Residues in contact with ARG 61 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57G GLU 2.9 16.5 + - - +
58G ILE* 3.8 6.3 - - - +
60G ARG* 1.3 76.2 - - - +
62G VAL* 1.3 57.2 + - - +
64G TYR* 3.4 6.1 + - - +
65G LEU* 2.9 31.2 + - - +
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Residues in contact with VAL 62 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18G LEU* 6.3 1.3 - - - -
21G LEU* 6.3 2.9 - - + -
22G TRP* 6.0 6.1 - - + -
58G ILE 2.9 19.0 + - - +
59G ASP* 3.7 5.6 - - - +
61G ARG* 1.3 74.9 - - - +
63G ARG* 1.3 66.4 + - - +
65G LEU* 3.3 6.0 + - - +
66G THR* 2.9 26.4 + - - -
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Residues in contact with ARG 63 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278D ARG* 6.2 4.0 - - - +
281D ARG* 4.0 11.7 + - - +
59G ASP 2.9 16.1 + - - +
60G ARG* 3.6 6.7 - - - +
62G VAL* 1.3 76.8 - - - +
64G TYR* 1.3 62.9 + - - +
66G THR* 3.3 2.5 + - - -
67G LYS* 2.9 24.8 + - - +
12N C 5.3 8.7 - - - +
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Residues in contact with TYR 64 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60G ARG 3.0 17.2 + - - +
61G ARG* 3.7 6.5 - - - +
63G ARG* 1.3 76.2 - - - +
65G LEU* 1.3 57.8 + - - +
67G LYS* 3.3 7.0 + - - +
68G CYS* 2.9 31.3 + - - +
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Residues in contact with LEU 65 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14G LEU* 5.4 6.5 - - + +
18G LEU* 4.2 25.8 - - + -
61G ARG 2.9 18.3 + - - +
62G VAL* 3.8 6.1 - - - +
64G TYR* 1.3 77.3 - - - +
66G THR* 1.3 57.8 + - - +
68G CYS* 3.3 5.9 + - - +
69G MET* 2.9 30.2 + - - +
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Residues in contact with THR 66 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281D ARG* 3.3 41.0 - - - +
282D LEU* 5.9 6.7 - - - -
285D LEU* 5.6 7.6 - - - +
62G VAL 2.9 16.8 + - - -
63G ARG* 4.7 0.2 - - - -
65G LEU* 1.3 76.2 - - - +
67G LYS* 1.3 64.8 + - - +
69G MET* 3.2 6.4 + - - +
70G GLU* 3.0 19.9 + - - +
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Residues in contact with LYS 67 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281D ARG* 3.2 18.3 - - - +
63G ARG 2.9 17.9 + - - +
64G TYR* 3.6 6.7 - - - +
66G THR* 1.3 75.7 - - - +
68G CYS* 1.3 58.1 + - - +
71G ASN* 2.9 39.2 + - + +
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Residues in contact with CYS 68 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14G LEU* 6.6 0.4 - - + -
64G TYR 2.9 17.4 + - - +
65G LEU* 3.8 5.6 - - - +
67G LYS* 1.3 76.6 - - - +
69G MET* 1.3 62.5 + - - +
72G LEU* 3.2 30.3 - - + +
109G ASP* 5.5 11.9 - - + -
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Residues in contact with MET 69 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285D LEU* 4.6 18.2 - - + -
15G LYS* 6.1 6.7 - - + -
65G LEU 2.9 17.9 + - - +
66G THR* 3.2 7.6 + - - +
68G CYS* 1.3 80.0 - - - +
70G GLU* 1.3 60.0 + - - +
72G LEU 4.4 4.0 - - - +
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Residues in contact with GLU 70 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281D ARG* 3.4 38.1 - - + +
285D LEU* 5.9 3.8 - - + -
66G THR 3.0 6.5 + - - +
67G LYS 4.3 0.4 - - - +
69G MET* 1.3 78.5 - - + +
71G ASN* 1.3 68.0 + - + +
72G LEU 3.3 8.0 - - - +
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Residues in contact with ASN 71 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4G PRO* 5.6 1.0 - - - +
67G LYS* 2.9 21.0 + - + +
70G GLU* 1.3 75.3 - - - +
72G LEU* 1.3 63.9 + - - +
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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