Contacts of the helix formed by residues 49 - 63 (chain K) 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 ARG 49 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1118A A 4.2 16.0 + - - +
1119A G 2.7 47.7 + - - +
1244A U 4.6 2.6 + - - -
48K GLY* 1.3 70.7 - - - -
50K GLU* 1.3 66.3 + - - +
51K GLU* 3.4 40.5 + - - +
52K GLN* 2.9 28.7 + - + +
53K ILE* 3.0 12.8 + - - +
55K GLU* 4.5 9.3 + - - -
128K LYS* 4.2 22.0 - - - +
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Residues in contact with GLU 50 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48K GLY 3.4 6.1 + - - -
49K ARG* 1.3 71.7 - - - +
51K GLU* 1.3 79.6 + - - +
53K ILE* 4.3 2.9 - - - -
54K VAL* 2.9 38.0 + - + +
129K PHE 5.2 1.6 - - - +
130K VAL* 3.5 40.0 - - + +
134K GLU* 4.8 13.8 - - - +
138K THR* 4.7 7.6 + - - -
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Residues in contact with GLU 51 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49K ARG* 2.9 42.8 + - - +
50K GLU* 1.3 93.1 + - - +
52K GLN* 1.3 61.4 + - - +
54K VAL* 3.9 4.0 - - - +
55K GLU* 3.1 29.7 + - - +
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Residues in contact with GLN 52 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1119A G 2.9 77.7 + - - +
1244A U 4.4 1.6 + - - -
8516A CL 3.8 9.6 - - - +
49K ARG* 2.9 35.0 + - + +
51K GLU* 1.3 75.2 - - - +
53K ILE* 1.3 84.9 + - + +
55K GLU* 3.0 21.9 + - - +
56K LYS* 3.1 12.0 + - - +
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Residues in contact with ILE 53 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1119A G 5.7 1.1 - - + +
46K ILE* 3.4 40.8 - - + +
47K THR 3.4 24.7 - - - +
48K GLY* 3.7 17.9 - - - +
49K ARG 3.0 9.3 + - - +
50K GLU* 3.8 6.5 - - - +
52K GLN* 1.3 98.9 - - - +
54K VAL* 1.3 65.3 + - + +
56K LYS* 3.0 13.3 + - - +
57K TYR* 3.3 23.2 - - + -
130K VAL* 4.1 13.0 - - + -
135K ILE* 4.0 20.9 - - + -
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Residues in contact with VAL 54 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50K GLU* 2.9 36.7 + - + +
51K GLU* 3.9 4.3 - - - +
53K ILE* 1.3 77.9 - - + +
55K GLU* 1.3 53.2 + - + +
57K TYR* 3.3 6.5 + - - +
58K GLU* 2.8 50.0 + - + +
130K VAL* 5.7 0.2 - - + -
135K ILE* 4.7 20.9 - - + -
138K THR* 3.5 39.7 - - + +
139K LEU* 4.8 2.0 - - + +
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Residues in contact with GLU 55 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49K ARG* 4.5 10.7 + - - -
51K GLU* 3.1 26.3 + - - +
52K GLN* 3.0 14.9 + - - +
54K VAL* 1.3 77.3 - - + +
56K LYS* 1.3 63.1 + - - +
58K GLU* 3.4 12.2 + - - +
59K LYS* 3.0 24.3 + - - +
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Residues in contact with LYS 56 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1236A A 4.0 20.7 - - + +
1237A U 4.5 7.7 + - - -
1241A G 5.0 0.2 + - - -
1242A A 3.2 36.2 + - - +
1243A C 5.5 0.2 - - - -
8516A CL 3.3 29.9 - - + +
52K GLN* 3.1 11.5 + - - +
53K ILE* 3.0 12.8 + - - +
55K GLU* 1.3 77.2 - - - +
57K TYR* 1.3 75.3 + - + +
59K LYS* 3.1 9.4 + - - +
60K ARG* 3.1 47.8 + - - +
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Residues in contact with TYR 57 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1242A A 4.0 18.7 + - - -
1243A C 5.0 2.4 + - - -
19K MET* 4.4 12.6 - - - -
46K ILE* 4.3 15.5 - - + +
53K ILE* 3.3 31.9 - - + +
54K VAL 3.3 5.7 + - - +
56K LYS* 1.3 92.8 - - + +
58K GLU* 1.3 65.5 + - - +
60K ARG* 3.2 17.4 + - - +
61K VAL* 3.1 24.3 + - - +
71K TYR* 3.1 36.1 - + + -
78K ILE* 3.8 23.3 - - + -
132K LEU* 6.0 0.2 - - + -
135K ILE* 4.4 19.1 - - + -
139K LEU* 4.1 17.5 - - + -
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Residues in contact with GLU 58 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2802A C 3.6 20.0 + - - -
2803A C 5.1 3.3 - - - +
54K VAL* 2.8 42.9 + - + +
55K GLU* 3.8 12.5 - - - +
57K TYR* 1.3 72.5 - - - +
59K LYS* 1.3 62.1 + - - +
61K VAL* 3.2 5.7 + - - +
62K ASP* 2.8 33.5 + - - +
138K THR* 4.2 14.6 - - + +
139K LEU* 3.6 22.3 - - + -
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Residues in contact with LYS 59 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1236A A 3.1 69.6 + - + +
55K GLU 3.0 14.1 + - - +
56K LYS* 3.2 12.3 - - - +
58K GLU* 1.3 77.4 - - - +
60K ARG* 1.3 57.8 + - - +
62K ASP* 3.0 12.1 + - + +
63K ILE* 2.8 45.1 + - + +
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Residues in contact with ARG 60 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1236A A 2.9 35.5 + - + +
1241A G 2.9 25.0 + - - -
1242A A 2.5 36.1 + - - -
56K LYS* 3.1 36.3 + - - +
57K TYR* 3.2 21.6 + - - +
59K LYS* 1.3 75.9 - - - +
61K VAL* 1.3 59.0 + - - +
63K ILE* 3.6 15.8 + - - +
69K TYR* 4.0 6.9 - - + -
71K TYR* 3.0 59.3 + - + +
8346K NA 2.9 17.3 - - - -
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Residues in contact with VAL 61 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2677A A 4.2 10.2 + - - +
2803A C 6.2 0.2 - - - +
57K TYR 3.1 14.1 + - - +
58K GLU* 3.4 8.7 - - - +
59K LYS 3.1 0.6 - - - -
60K ARG* 1.3 78.5 - - - +
62K ASP* 1.3 67.5 + - - +
63K ILE 3.3 1.0 - - - +
71K TYR* 4.3 17.3 - - + +
73K LYS* 3.9 41.1 - - + +
139K LEU* 4.2 19.7 - - + +
8346K NA 2.7 19.9 - - - -
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Residues in contact with ASP 62 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1235A G 5.9 0.9 - - - +
2678A A 5.7 1.0 + - - -
2802A C 5.6 0.2 - - - +
2803A C 4.6 11.3 + - - -
58K GLU* 2.8 22.2 + - - +
59K LYS* 3.0 15.2 + - + +
61K VAL* 1.3 82.2 - - - +
63K ILE* 1.3 67.5 - - - +
64K GLY* 3.6 1.2 + - - +
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Residues in contact with ILE 63 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1235A G 3.3 48.5 - - + +
1236A A 3.1 50.7 - - + +
59K LYS* 2.8 36.2 + - + +
60K ARG* 3.8 15.3 - - - +
61K VAL 3.3 1.3 - - - +
62K ASP* 1.3 80.0 - - - +
64K GLY* 1.3 63.6 + - - +
69K TYR* 4.0 13.2 - - + -
8346K NA 2.7 24.6 - - - -
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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