Contacts of the helix formed by residues 81 - 101 (chain S) 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 PRO 81 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2050A G 3.8 0.9 - - - +
2051A G 3.9 11.2 - - - +
27S HIS* 3.8 31.6 - - + +
31S ILE* 4.2 10.3 - - + -
50S VAL* 4.0 1.8 - - + -
57S VAL* 4.0 19.5 - - + -
59S PHE* 3.4 31.9 - - + -
79S ARG* 3.2 9.4 - - + +
80S TYR* 1.3 82.6 - - - +
82S GLU* 1.3 58.3 + - - +
83S LYS 3.5 2.0 - - - -
84S ALA* 4.5 1.8 - - + -
85S SER* 2.6 33.8 + - - -
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Residues in contact with GLU 82 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2050A G 3.2 36.7 + - - +
2051A G 3.5 9.0 + - - +
51S ILE* 4.2 29.9 - - + +
80S TYR 2.7 11.6 + - - +
81S PRO* 1.3 69.4 - - - +
83S LYS* 1.3 69.0 + - - +
85S SER* 3.5 6.3 - - - -
86S LYS* 2.8 63.1 + - - +
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Residues in contact with LYS 83 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1433A G 4.6 9.9 + - - -
2051A G 3.1 33.4 + - - +
2052A U 2.8 36.4 + - - +
22S GLN* 3.4 24.6 + - - +
23S MET* 4.6 11.7 - - + -
24S SER 5.6 0.9 - - - +
27S HIS* 6.2 0.2 - - - +
82S GLU* 1.3 85.0 - - - +
84S ALA* 1.3 65.2 - - - +
86S LYS* 3.0 19.5 + - + +
87S ALA* 3.0 13.1 + - + +
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Residues in contact with ALA 84 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2051A G 4.6 0.8 + - - -
23S MET* 4.0 19.0 - - + +
24S SER 4.7 2.7 - - - +
27S HIS* 3.9 23.5 + - + +
28S SER* 4.3 14.6 - - - +
31S ILE* 3.5 20.4 - - + -
81S PRO* 3.9 3.8 + - + +
82S GLU 3.5 0.2 - - - -
83S LYS* 1.3 79.1 - - - +
85S SER* 1.3 58.3 + - - +
87S ALA* 3.1 2.6 + - - +
88S PHE* 2.9 33.6 + - + -
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Residues in contact with SER 85 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31S ILE* 3.6 15.1 - - - +
47S LEU* 3.9 16.7 - - - +
50S VAL* 3.5 16.6 - - - +
51S ILE* 3.8 20.6 - - - -
81S PRO 2.6 24.7 + - - -
82S GLU* 3.5 5.2 - - - -
84S ALA* 1.3 78.8 - - - +
86S LYS* 1.3 61.5 + - - +
88S PHE* 3.2 6.3 + - - +
89S LEU* 3.0 26.5 + - - +
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Residues in contact with LYS 86 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51S ILE* 3.5 29.8 - - + -
82S GLU* 2.8 51.4 + - - +
83S LYS* 3.0 9.6 + - - +
85S SER* 1.3 77.2 - - - +
87S ALA* 1.3 63.6 + - - +
89S LEU* 3.2 8.9 + - + +
90S ASP* 3.1 25.2 + - - +
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Residues in contact with ALA 87 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18S LEU* 3.3 17.6 - - + +
21S ARG* 3.2 30.5 - - - +
23S MET* 3.6 24.7 - - + -
83S LYS 3.0 10.0 + - - +
84S ALA 3.1 8.3 + - - +
86S LYS* 1.3 77.2 - - - +
88S PHE* 1.3 57.8 + - - +
90S ASP* 3.3 7.5 + - - +
91S LEU 3.0 20.3 + - - -
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Residues in contact with PHE 88 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18S LEU* 4.7 1.3 - - + -
23S MET* 4.1 13.9 - - + -
28S SER* 3.8 41.7 - - - -
31S ILE* 3.8 22.4 - - + -
32S ALA* 4.1 10.1 - - + -
35S ILE* 4.2 13.5 - - + -
47S LEU* 3.6 19.5 - - + -
84S ALA 2.9 28.2 + - - +
85S SER* 3.6 3.6 - - - +
86S LYS 3.2 0.2 - - - -
87S ALA* 1.3 78.1 - - - +
89S LEU* 1.3 59.3 + - - +
91S LEU* 3.1 16.5 + - + +
92S LEU* 2.8 34.8 + - + +
114S VAL* 4.1 19.1 - - + -
116S ALA* 4.9 0.7 - - + -
143S VAL* 4.2 20.4 - - + -
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Residues in contact with LEU 89 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44S VAL* 3.8 38.1 - - + +
47S LEU* 3.7 24.2 - - + -
48S GLU* 4.0 20.0 - - + +
51S ILE* 3.7 28.5 - - + -
85S SER 3.0 14.5 + - - +
86S LYS* 3.2 10.7 + - + +
88S PHE* 1.3 73.4 - - - +
90S ASP* 1.3 63.2 + - - +
92S LEU* 3.3 3.7 + - + +
93S GLU* 2.8 31.4 + - - +
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Residues in contact with ASP 90 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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496A G 5.1 6.4 - - - +
18S LEU* 4.6 2.5 - - + -
21S ARG* 3.3 25.8 + - - +
86S LYS 3.1 13.5 + - - +
87S ALA* 3.3 10.5 - - - +
89S LEU* 1.3 79.5 - - - +
91S LEU* 1.3 63.0 + - - +
93S GLU* 3.2 18.1 + - - +
94S ASN* 3.1 23.6 + - - +
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Residues in contact with LEU 91 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16S ALA* 3.7 8.1 - - + +
17S MET* 3.5 46.0 - - - +
18S LEU* 3.7 11.9 - - + +
87S ALA 3.0 13.6 + - - +
88S PHE* 3.1 21.3 + - + +
90S ASP* 1.3 76.9 - - - +
92S LEU* 1.3 57.6 + - + +
94S ASN* 3.3 7.9 + - + +
95S ALA* 3.0 26.7 + - - +
114S VAL* 5.2 1.3 - - + -
143S VAL* 3.7 35.7 - - + +
144S GLU 4.7 0.2 - - - +
145S LEU* 4.0 24.9 - - + -
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Residues in contact with LEU 92 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35S ILE* 4.6 7.6 - - + -
40S ALA* 4.3 17.9 - - + +
43S ALA* 3.7 25.1 - - + -
44S VAL* 4.3 20.9 - - + -
47S LEU* 4.0 19.5 - - + -
88S PHE* 2.8 24.4 + - + +
89S LEU* 3.8 4.7 - - + +
91S LEU* 1.3 71.2 - - + +
93S GLU* 1.3 61.3 + - - +
95S ALA* 4.3 2.9 - - + -
96S VAL* 2.9 37.9 + - + +
111S ILE* 4.1 18.2 - - + -
145S LEU* 3.5 25.4 - - + -
147S LEU* 5.1 1.3 - - + -
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Residues in contact with GLU 93 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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493A U 4.5 4.2 + - - +
494A C 3.8 40.7 + - - +
495A A 5.5 1.4 + - - -
44S VAL* 5.9 0.2 - - - +
89S LEU 2.8 18.1 + - - +
90S ASP* 3.5 18.6 - - - +
92S LEU* 1.3 76.8 - - - +
94S ASN* 1.3 57.6 + - - +
96S VAL* 4.2 3.2 - - - +
97S GLY* 3.2 22.5 + - - -
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Residues in contact with ASN 94 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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493A U 4.1 12.6 + - - +
499A G 3.2 20.7 + - - +
500A G 2.7 55.7 + - - +
16S ALA* 3.6 10.1 - - + +
17S MET 4.6 2.5 + - - +
90S ASP 3.1 11.6 + - - +
91S LEU* 3.5 10.3 - - + +
93S GLU* 1.3 76.4 - - - +
95S ALA* 1.3 58.8 + - - +
97S GLY* 3.1 1.9 + - - -
98S ASN* 2.8 50.1 + - - -
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Residues in contact with ALA 95 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14S ALA* 4.3 1.9 - - - +
15S LYS 4.2 5.4 - - - +
16S ALA* 3.5 25.4 - - + -
91S LEU 3.0 12.7 + - - +
92S LEU* 3.9 3.6 - - - +
94S ASN* 1.3 77.0 - - - +
96S VAL* 1.3 52.9 + - - +
98S ASN* 3.0 6.7 + - - +
99S ALA* 2.8 34.7 + - - +
145S LEU* 4.1 15.0 - - + -
147S LEU* 3.6 23.2 - - + +
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Residues in contact with VAL 96 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40S ALA* 3.6 31.9 - - + -
44S VAL* 5.7 3.4 - - + -
92S LEU* 2.9 28.6 + - + +
93S GLU* 4.3 4.3 - - - +
95S ALA* 1.3 71.6 - - - +
97S GLY* 1.3 57.7 + - - +
99S ALA* 3.3 8.4 - - - +
100S ASP* 3.0 45.3 + - - +
106S GLY* 3.8 16.4 - - - -
107S GLU* 3.8 17.0 - - + +
147S LEU* 4.2 4.9 - - + -
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Residues in contact with GLY 97 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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492A C 4.9 2.1 + - - -
493A U 5.3 14.5 - - - +
93S GLU 3.2 14.3 + - - -
94S ASN* 3.1 6.6 + - - -
95S ALA 3.1 0.8 - - - -
96S VAL* 1.3 76.6 - - - +
98S ASN* 1.3 65.9 + - - +
100S ASP* 3.3 7.9 + - - +
101S HIS* 3.1 23.6 + - - +
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Residues in contact with ASN 98 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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492A C 4.5 2.8 + - - -
493A U 5.2 3.2 + - - -
500A G 3.1 27.3 - - - +
501A G 2.8 40.6 + - - +
14S ALA* 5.1 2.2 - - + -
15S LYS 3.1 19.4 - - - +
94S ASN* 2.8 32.8 + - - +
95S ALA 3.4 6.1 - - - +
97S GLY* 1.3 76.2 - - - +
99S ALA* 1.3 61.9 + - - +
101S HIS* 3.2 15.8 + - - +
102S GLN* 3.3 24.7 + - - +
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Residues in contact with ALA 99 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14S ALA* 4.0 16.1 - - + +
95S ALA 2.8 14.2 + - - +
96S VAL* 3.3 12.3 - - - +
98S ASN* 1.3 77.6 - - - +
100S ASP* 1.3 61.5 + - - +
102S GLN* 3.1 7.0 + - - +
104S PHE* 3.1 31.8 + - - -
106S GLY* 3.8 4.7 - - - -
109S MET* 3.0 34.1 - - + -
147S LEU* 4.4 0.9 - - + -
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Residues in contact with ASP 100 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96S VAL* 3.0 32.0 + - - +
97S GLY* 3.7 7.2 - - - +
98S ASN 3.3 0.4 - - - -
99S ALA* 1.3 71.8 - - - +
101S HIS* 1.3 58.9 + - - +
102S GLN 2.8 11.3 + - - -
103S GLY* 2.9 14.2 + - - -
104S PHE 3.1 18.3 - - - +
105S ASP* 4.2 1.7 - - - +
106S GLY 3.2 14.1 + - - -
107S GLU* 5.9 0.2 - - - +
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Residues in contact with HIS 101 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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491A C 4.5 9.2 + - - -
492A C 3.2 54.6 + - - +
501A G 4.3 13.6 + - - -
502A A 6.0 2.7 - - - -
97S GLY 3.1 16.8 + - - +
98S ASN* 3.2 8.9 + - - +
100S ASP* 1.3 74.8 - - - +
102S GLN* 1.3 62.5 + - + +
103S GLY 3.5 0.2 - - - -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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