Contacts of the helix formed by residues 96 - 109 (chain N) 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 96 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401A C 3.4 35.4 + - - +
402A U 3.3 18.2 - - - +
95N LYS* 1.3 76.4 - - - +
97N ILE* 1.3 66.3 + - - +
98N GLN* 3.7 25.4 + - - +
99N ARG* 2.9 33.9 + - - +
100N ILE* 3.2 10.7 + - - +
166N ALA* 4.6 7.9 + - - +
169N ARG* 5.9 0.8 - - - +
170N CYS* 3.8 16.1 - - - +
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Residues in contact with ILE 97 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402A U 2.8 28.7 + - - +
403A C 4.1 4.5 - - - +
67N ILE* 3.5 28.7 - - + -
68N ARG* 3.5 34.8 - - - +
69N LYS* 4.1 7.6 - - - -
70N GLY 4.5 1.8 - - - +
95N LYS 3.9 0.4 + - - -
96N ASN* 1.3 71.9 - - - +
98N GLN* 1.3 59.3 + - - +
100N ILE* 2.9 13.2 + - + +
101N ALA* 2.8 26.9 + - - +
127N LYS* 3.6 35.0 - - + +
129N HIS* 4.0 16.4 - - + -
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Residues in contact with GLN 98 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96N ASN* 3.2 17.0 + - - +
97N ILE* 1.3 78.3 - - - +
99N ARG* 1.3 59.3 + - - +
101N ALA* 3.4 3.0 + - - +
102N GLU* 3.0 27.1 + - - +
117N SER* 2.6 47.8 + - - +
118N TYR* 3.8 6.0 - - - +
119N SER* 5.3 0.8 - - - -
129N HIS* 3.5 33.9 + - + +
165N SER* 5.1 1.6 + - - -
166N ALA* 3.9 20.4 - - + +
169N ARG* 4.3 12.2 + - - +
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Residues in contact with ARG 99 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A C 3.2 24.2 + - - -
157A G 2.9 31.1 + - - -
95N LYS* 3.7 22.7 - - + +
96N ASN* 2.9 19.6 + - - +
98N GLN* 1.3 78.6 - - - +
100N ILE* 1.3 65.1 + - - +
102N GLU* 3.4 11.2 + - + +
103N GLU* 3.1 27.9 + - + +
159N THR* 4.2 9.6 + - + +
162N GLY* 3.9 16.3 - - - -
164N THR* 4.6 2.9 - - - -
166N ALA* 3.7 7.6 - - + -
167N GLY* 3.3 40.9 + - - +
170N CYS* 3.5 23.6 - - - +
171N ARG* 4.3 1.8 - - - +
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Residues in contact with ILE 100 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1470A A 3.6 35.9 - - - +
1471A A 3.4 25.1 - - - +
67N ILE* 4.1 13.2 - - + -
68N ARG* 4.7 10.1 - - - +
93N ARG* 5.7 1.1 - - + -
95N LYS* 4.5 21.1 - - + +
96N ASN 3.2 9.6 + - - +
97N ILE* 2.9 20.9 + - + +
99N ARG* 1.3 73.1 - - - +
101N ALA* 1.3 68.0 + - - +
103N GLU* 3.1 7.7 + - + +
104N ARG* 2.9 39.9 + - - +
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Residues in contact with ALA 101 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65N VAL* 3.8 21.2 - - + +
67N ILE* 3.8 22.8 - - + +
97N ILE 2.8 12.1 + - - +
98N GLN 3.5 9.9 - - - +
100N ILE* 1.3 76.7 - - - +
102N GLU* 1.3 63.4 + - - +
104N ARG* 3.2 1.6 + - - -
105N ALA* 3.0 24.3 + - - +
129N HIS* 4.1 22.9 - - + +
131N VAL* 4.4 4.3 - - + -
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Residues in contact with GLU 102 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98N GLN* 3.0 18.6 + - - +
99N ARG* 3.7 10.7 - - + +
100N ILE 3.2 0.2 - - - -
101N ALA* 1.3 76.7 - - - +
103N GLU* 1.3 55.9 + - - +
105N ALA* 3.4 1.7 + - - +
106N ASN* 2.9 29.6 + - - +
114N VAL* 4.0 11.4 - - + +
116N ASN 3.9 0.9 - - - -
117N SER* 2.4 42.3 + - - +
131N VAL* 4.0 9.6 - - + -
159N THR* 3.9 14.4 - - + +
164N THR* 2.6 37.3 + - - +
165N SER* 3.5 14.9 + - - -
166N ALA* 4.2 7.5 - - - +
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Residues in contact with GLU 103 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A C 4.8 2.1 + - - -
1470A A 5.1 0.9 - - - -
1471A A 4.5 8.1 - - - +
95N LYS* 3.1 37.6 + - - +
99N ARG* 3.1 20.6 + - + +
100N ILE* 3.1 8.9 + - + +
102N GLU* 1.3 77.4 - - - +
104N ARG* 1.3 64.9 + - + +
106N ASN* 3.2 4.7 + - - +
107N ARG* 2.9 57.1 + - - +
159N THR* 4.3 21.3 - - - +
160N PHE* 3.8 25.3 - - + +
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Residues in contact with ARG 104 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1468A G 4.2 16.6 + - - -
1469A C 3.0 49.7 + - - +
1470A A 5.0 2.6 + - - -
1471A A 2.8 40.8 + - - +
36N ALA* 5.8 4.9 - - + +
37N VAL* 4.2 2.5 - - + -
65N VAL* 4.3 10.1 - - + -
66N ALA 3.9 7.0 + - - -
67N ILE* 2.9 43.2 - - - +
68N ARG* 4.8 2.6 - - - +
100N ILE* 2.9 24.2 + - - +
101N ALA 3.2 3.8 + - - +
103N GLU* 1.3 76.1 - - + +
105N ALA* 1.3 63.7 + - - +
107N ARG* 3.3 6.8 + - - +
108N LYS* 2.8 46.2 + - - +
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Residues in contact with ALA 105 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37N VAL* 4.2 5.2 - - + -
63N VAL* 5.1 1.1 - - + -
65N VAL* 3.6 21.8 - - + +
101N ALA 3.0 13.2 + - - +
102N GLU 3.5 7.9 - - - +
104N ARG* 1.3 75.8 - - - +
106N ASN* 1.3 65.5 + - - +
108N LYS* 2.8 19.0 + - - +
109N PHE* 3.1 20.9 - - + -
131N VAL* 3.9 22.7 - - + -
133N LEU* 4.2 8.3 - - + -
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Residues in contact with ASN 106 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102N GLU 2.9 16.7 + - - +
103N GLU 3.6 4.9 - - - +
105N ALA* 1.3 77.3 - - - +
107N ARG* 1.3 61.3 + - - +
109N PHE 3.0 12.8 + - - -
110N PRO 3.4 0.3 - - - -
112N LEU 3.6 8.3 + - - -
113N ARG* 3.9 0.4 - - - +
114N VAL* 3.2 18.0 - - + +
133N LEU* 3.9 10.2 - - - +
157N LEU* 4.5 0.5 - - - +
159N THR* 3.8 5.8 - - - +
160N PHE* 3.1 25.7 - - + -
8347N NA 2.3 38.5 - - - -
8518N CL 2.7 31.1 - - - +
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Residues in contact with ARG 107 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A U 4.6 1.0 + - - -
181A G 3.4 28.9 + - - -
1471A A 3.4 43.4 + - - -
1472A C 3.3 22.8 + - - -
103N GLU* 2.9 45.5 + - - +
104N ARG* 3.7 8.6 - - - +
105N ALA 3.2 0.2 - - - -
106N ASN* 1.3 77.8 - - - +
108N LYS* 1.3 76.2 + - - +
109N PHE 3.2 0.7 + - - -
110N PRO* 3.3 15.2 - - - +
160N PHE* 3.5 25.5 - - + -
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Residues in contact with LYS 108 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A U 2.8 26.0 + - - -
134A U 3.7 12.0 - - - +
1467A C 6.2 0.2 - - - -
1469A C 5.0 9.1 - - - +
1472A C 5.6 1.6 + - - -
36N ALA* 5.8 4.0 - - - -
37N VAL* 3.2 38.6 - - + -
104N ARG* 2.8 38.4 - - - +
105N ALA 2.8 7.4 + - - +
107N ARG* 1.3 91.8 - - - +
109N PHE* 1.3 71.4 + - + +
110N PRO* 3.0 0.7 - - - +
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Residues in contact with PHE 109 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A U 3.4 41.7 - - - +
135A G 3.8 9.6 - - - -
37N VAL* 3.8 20.4 - - + -
39N ARG* 4.3 10.5 - - + -
61N ILE* 4.6 6.5 - - + -
63N VAL* 3.4 38.1 - - + -
105N ALA 3.1 19.7 - - - -
106N ASN 3.0 8.6 + - - +
108N LYS* 1.3 82.9 - - + +
110N PRO* 1.3 52.9 - - - -
111N ASN* 2.7 17.8 + - - -
112N LEU* 2.7 41.0 + - + +
133N LEU* 3.8 13.9 - - + -
8347N NA 2.9 6.9 - - - -
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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
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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) + - + + + + + -
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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