Contacts of the helix formed by residues 55 - 77 (chain G) in PDB entry 1NJI
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 55 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1139A U 4.7 1.6 - - - +
1140A C 3.3 23.8 - - - +
53G GLU* 3.7 25.3 + - - +
54G ASP* 1.3 78.8 - - - +
56G ALA* 1.3 56.7 + - - +
57G LYS* 3.3 11.1 + - - +
58G THR* 2.8 45.1 + - - -
59G MET* 3.0 9.8 + - - -
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Residues in contact with ALA 56 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1139A U 3.9 29.6 - - - +
1140A C 2.8 24.4 + - - +
2784A A 3.7 16.2 + - - +
54G ASP 3.7 1.2 + - - -
55G ASN* 1.3 71.1 - - - +
57G LYS* 1.3 56.7 + - - +
59G MET* 3.4 5.8 + - - +
60G SER* 2.6 34.7 + - - -
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Residues in contact with LYS 57 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1117A A 4.2 37.2 + - - +
1118A A 5.2 2.6 + - - -
1138A G 3.7 24.2 + - - -
1139A U 4.1 23.0 + - - +
2792A A 4.5 21.6 - - - +
35G TYR* 3.6 20.4 + - - +
55G ASN* 3.0 9.6 + - - +
56G ALA* 1.3 76.7 - - - +
58G THR* 1.3 61.2 + - - +
60G SER* 3.4 17.6 - - - -
61G THR* 3.4 13.7 + - - -
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Residues in contact with THR 58 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35G TYR* 4.4 14.9 - - - -
36G PRO 4.9 2.4 + - - -
38G ILE* 4.0 8.5 - - + +
51G SER* 3.9 13.5 - - - +
53G GLU* 3.5 36.4 + - - +
55G ASN* 2.8 37.0 + - - -
57G LYS* 1.3 68.0 - - - +
59G MET* 1.3 66.7 + - - +
60G SER 3.0 2.0 + - - -
61G THR* 3.2 4.0 + - - -
62G ILE* 3.0 37.4 + - + +
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Residues in contact with MET 59 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2783A A 3.7 3.2 + - - -
2784A A 4.4 18.5 - - - +
1G PRO* 3.8 37.7 - - + -
53G GLU 4.4 2.0 - - - +
54G ASP* 3.5 30.3 - - + +
55G ASN 3.0 5.5 + - - +
56G ALA* 3.8 8.3 - - - +
58G THR* 1.3 78.0 - - - +
60G SER* 1.3 62.9 + - - +
62G ILE* 3.4 14.1 + - + +
63G GLY* 3.1 18.9 + - - -
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Residues in contact with SER 60 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1139A U 5.3 1.6 + - - -
2783A A 2.7 43.7 + - - -
2784A A 3.2 21.0 + - - -
2792A A 3.9 13.7 - - - -
56G ALA 2.6 24.2 + - - -
57G LYS* 3.4 9.6 - - - -
58G THR 3.0 0.2 - - - -
59G MET* 1.3 77.3 - - - +
61G THR* 1.3 62.2 + - - +
64G THR* 3.1 17.2 + - - -
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Residues in contact with THR 61 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2792A A 3.8 12.0 + - - -
2793A A 4.3 6.7 - - - +
35G TYR* 3.1 43.5 - - + -
38G ILE* 3.7 11.4 - - + -
57G LYS 3.4 4.0 + - - -
58G THR 3.2 3.2 + - - -
60G SER* 1.3 74.8 - - - +
62G ILE* 1.3 56.8 + - - +
64G THR* 2.8 8.1 + - - -
65G PHE* 2.7 71.8 + - + -
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Residues in contact with ILE 62 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1G PRO* 4.1 26.9 - - + +
3G VAL* 4.0 26.9 - - + -
38G ILE* 3.8 15.3 - - + -
49G ILE* 4.2 24.3 - - + +
50G GLU* 5.0 1.3 - - - -
51G SER* 4.4 14.1 - - - +
58G THR* 3.0 32.4 + - + +
59G MET* 3.6 17.9 - - + +
61G THR* 1.3 77.7 - - - +
63G GLY* 1.3 64.2 + - - +
65G PHE* 3.1 2.7 + - - +
66G GLN* 3.0 22.5 + - - +
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Residues in contact with GLY 63 (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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2783A A 3.5 33.1 - - - +
2784A A 5.6 1.1 - - - -
59G MET 3.1 10.4 + - - -
62G ILE* 1.3 80.8 - - - +
64G THR* 1.3 61.6 + - - +
66G GLN* 3.4 11.0 + - - +
67G SER* 3.2 17.7 + - - -
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Residues in contact with THR 64 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2782A G 2.6 28.0 + - - +
2783A A 3.0 10.4 + - - -
2792A A 3.0 20.5 + - - +
2793A A 3.6 23.6 - - + +
60G SER 3.1 7.3 + - - -
61G THR* 2.8 10.4 + - - +
63G GLY* 1.3 74.6 - - - +
65G PHE* 1.3 68.1 + - + +
67G SER* 3.4 2.6 + - - -
68G HIS* 3.0 48.5 + - + +
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Residues in contact with PHE 65 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2793A A 4.3 15.9 - + - -
33G LEU* 3.7 57.7 - - + -
34G TRP 3.8 4.5 - - - -
35G TYR* 3.8 8.7 - - + -
38G ILE* 3.6 37.2 - - + -
40G VAL* 4.2 11.7 - - + -
49G ILE* 3.6 19.7 - - + -
61G THR* 2.7 44.1 + - + +
62G ILE 3.6 2.2 - - - +
64G THR* 1.3 77.0 - - + +
66G GLN* 1.3 67.0 + - - +
68G HIS* 3.1 6.2 + + - +
69G ILE* 2.9 24.8 + - - +
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Residues in contact with GLN 66 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3G VAL* 3.9 25.8 - - + +
5G LEU* 3.7 25.0 - - + +
49G ILE* 3.6 12.7 - - + +
62G ILE* 3.0 12.2 + - - +
63G GLY* 3.4 14.0 - - - +
65G PHE* 1.3 75.9 - - - +
67G SER* 1.3 66.1 + - - +
69G ILE* 2.9 14.6 + - - +
70G GLU* 3.0 37.3 + - - +
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Residues in contact with SER 67 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2782A G 3.4 19.1 - - - -
2783A A 2.5 34.3 + - - -
63G GLY 3.2 8.0 + - - -
64G THR 3.4 2.2 + - - -
66G GLN* 1.3 81.2 + - - +
68G HIS* 1.3 58.1 + - - +
70G GLU* 4.1 13.4 + - - +
71G ASN* 3.0 40.1 + - - +
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Residues in contact with HIS 68 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2781A U 3.4 27.9 + - + -
2782A G 3.8 18.6 - - - -
2793A A 3.0 29.4 + + - -
2794A G 6.2 0.4 - - - -
31G ARG* 2.7 34.6 + - - +
33G LEU* 4.7 7.9 - - + -
64G THR* 3.0 36.4 + - + +
65G PHE* 3.4 12.8 - + - +
66G GLN 2.9 0.2 + - - -
67G SER* 1.3 77.0 - - - +
69G ILE* 1.3 60.9 + - + +
71G ASN* 3.5 7.4 + - - +
72G MET* 3.0 30.1 + - + +
138G ILE* 6.0 1.6 - - - +
139G GLU* 4.2 4.9 + - - +
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Residues in contact with ILE 69 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5G LEU* 3.7 12.1 - - + -
20G ILE* 4.2 8.5 - - + -
22G VAL* 5.4 0.4 - - + -
33G LEU* 4.0 18.6 - - + -
40G VAL* 4.2 0.2 - - + -
47G VAL* 4.0 25.1 - - + -
49G ILE* 3.6 29.8 - - + -
65G PHE 2.9 7.2 + - - +
66G GLN 2.9 6.3 + - - +
68G HIS* 1.3 75.2 - - - +
70G GLU* 1.3 66.1 + - - +
72G MET* 2.8 38.0 + - + +
73G PHE* 2.9 41.7 + - + -
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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
----------------------------------------------------------
5G LEU* 3.6 26.8 - - + +
66G GLN* 3.0 39.8 + - - +
67G SER* 4.1 13.9 + - - +
69G ILE* 1.3 74.4 - - - +
71G ASN* 1.3 66.3 + - - +
73G PHE* 3.0 19.1 + - + +
74G HIS* 3.0 22.5 + - - +
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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
----------------------------------------------------------
2781A U 3.7 4.0 + - - -
2782A G 2.8 32.3 + - - -
67G SER* 3.0 27.5 + - - +
68G HIS* 3.5 8.8 + - - +
69G ILE 3.1 0.2 - - - -
70G GLU* 1.3 80.2 - - - +
72G MET* 1.3 57.2 + - + +
74G HIS* 3.4 0.8 + - - -
75G GLY 3.0 20.6 + - - -
80G TRP* 3.1 35.4 + - + -
138G ILE* 3.4 33.8 - - + +
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Residues in contact with MET 72 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20G ILE* 4.7 16.2 - - + +
22G VAL* 3.9 34.3 - - + -
29G VAL* 4.4 24.2 - - + +
31G ARG* 3.6 35.9 - - + -
33G LEU* 5.2 2.0 - - + -
68G HIS* 3.0 12.1 - - + +
69G ILE* 2.8 50.2 + - + +
71G ASN* 1.3 70.8 - - + +
73G PHE* 1.3 68.0 + - - +
75G GLY* 3.0 11.4 + - - -
76G VAL* 3.0 20.1 + - - +
136G PRO 4.7 5.6 - - - +
138G ILE* 6.4 0.9 - - + -
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Residues in contact with PHE 73 (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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5G LEU* 4.3 14.8 - - + -
6G GLU 4.2 6.1 - - - -
7G ILE* 3.9 28.7 - - + -
8G PRO* 3.7 33.4 - - + -
11G VAL* 4.7 3.6 - - + -
13G ALA* 4.5 7.4 - - + -
22G VAL* 3.9 23.8 - - + -
47G VAL* 4.2 11.2 - - + -
69G ILE* 2.9 37.9 + - + -
70G GLU* 3.2 21.3 - - + +
72G MET* 1.3 76.2 - - - +
74G HIS* 1.3 62.4 + - - +
76G VAL* 3.0 23.4 - - - +
77G THR* 3.2 14.2 + - - +
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Residues in contact with HIS 74 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70G GLU 3.0 10.8 + - - +
71G ASN* 3.6 9.2 - - - +
73G PHE* 1.3 78.4 - - - +
75G GLY* 1.3 52.2 + - - +
77G THR* 3.7 5.3 + - - -
78G GLU* 3.1 45.2 + - + +
79G GLY 2.7 57.0 + - - -
80G TRP* 3.7 34.0 - + + -
172G PRO* 6.2 0.4 - - - +
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Residues in contact with GLY 75 (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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26G ASN* 2.6 33.3 + - - -
71G ASN 3.0 10.5 + - - -
72G MET 3.0 2.6 + - - -
74G HIS* 1.3 78.3 - - - +
76G VAL* 1.3 53.4 + - - +
79G GLY* 3.4 4.4 - - - -
80G TRP* 3.5 16.4 - - - +
136G PRO* 3.2 31.3 - - - +
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Residues in contact with VAL 76 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11G VAL* 3.6 20.4 - - + -
22G VAL* 3.2 46.0 - - + +
24G GLY* 3.3 19.4 - - - +
25G ASP 3.3 0.9 + - - -
26G ASN* 2.7 34.0 + - - -
27G GLY 3.4 16.8 - - - +
28G SER* 4.2 2.0 - - - -
29G VAL* 4.3 10.5 - - + +
72G MET 3.0 11.9 + - - +
73G PHE 3.0 18.6 - - - +
75G GLY* 1.3 77.6 - - - +
77G THR* 1.3 55.6 + - - +
136G PRO* 4.5 0.7 - - + -
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Residues in contact with THR 77 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8G PRO* 5.1 4.7 - - + -
10G ASP* 3.7 27.6 - - + +
11G VAL* 3.4 26.9 - - + -
25G ASP* 5.9 1.7 - - - +
26G ASN* 3.5 15.6 + - - +
73G PHE 3.2 19.0 + - - +
74G HIS* 3.3 8.7 + - - -
75G GLY 3.3 0.4 - - - -
76G VAL* 1.3 79.0 - - - +
78G GLU* 1.3 78.8 + - - +
79G GLY 3.2 1.0 + - - -
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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