Contacts of the strand formed by residues 60 - 68 (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 ILE 60 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A C 5.2 0.9 + - - -
39N ARG* 5.0 4.0 + - - -
53N GLY 4.9 0.2 - - - +
54N TYR* 3.8 26.9 - - + -
55N LYS* 2.8 53.8 - - + +
57N LYS* 3.3 24.9 + - + +
58N GLN 3.3 1.0 - - - -
59N GLY* 1.3 80.4 + - - +
61N ILE* 1.3 67.8 + - - +
62N VAL* 4.5 0.3 + - - +
132N ILE* 4.4 7.2 - - + -
133N LEU 3.7 3.4 - - - +
134N ILE* 3.7 20.2 - - + -
141N ILE* 4.4 7.6 - - + -
147N LEU* 4.0 16.4 - - + -
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Residues in contact with ILE 61 (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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135A G 3.6 29.2 - - - +
136A C 4.5 1.8 - - - +
39N ARG* 3.9 33.2 - - - +
59N GLY* 3.5 20.2 - - - +
60N ILE* 1.3 83.0 - - - +
62N VAL* 1.3 70.0 + - - +
63N VAL* 3.6 23.3 - - + -
109N PHE* 4.6 3.6 - - + -
112N LEU* 4.0 27.4 - - + -
131N VAL 3.7 0.2 - - - +
132N ILE* 3.4 4.7 - - - +
133N LEU* 2.6 43.5 + - + +
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Residues in contact with VAL 62 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39N ARG* 3.6 4.2 - - - +
40N ILE* 3.0 55.9 + - + +
41N GLU 5.7 1.6 - - - +
43N PRO* 3.9 20.2 - - + -
54N TYR* 3.7 36.1 - - + -
60N ILE 5.5 0.4 - - - +
61N ILE* 1.3 79.3 - - - +
63N VAL* 1.3 73.5 + - - +
118N TYR* 4.7 1.1 - - - +
130N GLU* 4.3 13.2 - - + -
131N VAL 3.3 9.0 - - - +
132N ILE* 4.7 10.3 - - + -
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Residues in contact with VAL 63 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37N VAL* 3.2 28.5 - - + -
38N VAL 2.9 33.4 - - - +
39N ARG* 3.5 3.6 - - - +
40N ILE* 4.3 1.1 - - - +
61N ILE* 3.6 11.4 - - + -
62N VAL* 1.3 85.5 - - - +
64N ARG* 1.3 61.5 + - - +
65N VAL* 3.8 1.0 + - + +
105N ALA* 5.1 3.4 - - + -
109N PHE* 3.4 31.0 - - + -
129N HIS 3.5 0.5 - - - +
130N GLU* 3.2 5.4 - - - -
131N VAL* 2.7 40.1 + - - +
133N LEU* 3.9 9.2 - - + -
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Residues in contact with ARG 64 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55H GLN* 5.5 5.7 - - - +
31N TRP* 3.0 57.8 - - - +
34N GLU* 3.0 26.6 + - - -
35N PRO 5.4 0.2 - - - +
36N ALA 3.8 1.0 - - - +
37N VAL* 3.6 4.0 - - - -
38N VAL* 2.9 37.0 + - + +
40N ILE* 3.8 26.1 - - + +
44N THR* 3.8 6.3 + - - -
63N VAL* 1.3 73.2 - - - +
65N VAL* 1.3 62.8 + - - +
66N ALA 4.3 0.2 - - - -
120N VAL* 4.4 1.8 - - + -
128N TRP* 4.0 26.0 - - + -
129N HIS 3.4 7.2 - - - +
130N GLU* 3.3 31.6 + - + +
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Residues in contact with VAL 65 (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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36N ALA* 3.3 10.5 - - + +
37N VAL* 4.0 13.9 - - + -
63N VAL* 4.4 2.5 - - + +
64N ARG* 1.3 81.0 - - - +
66N ALA* 1.3 72.6 + - - +
67N ILE* 3.8 18.6 - - + +
101N ALA* 3.8 20.6 - - + +
104N ARG* 4.3 9.9 - - + -
105N ALA* 3.6 31.2 - - + -
127N LYS 3.5 1.7 - - - +
128N TRP* 3.3 8.7 - - - -
129N HIS* 2.8 35.9 + - - +
131N VAL* 4.4 7.2 - - + -
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Residues in contact with ALA 66 (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 4.4 8.9 + - - +
35N PRO 4.4 11.4 + - - +
36N ALA* 3.0 18.9 + - - +
64N ARG 4.3 0.2 - - - -
65N VAL* 1.3 72.4 - - - +
67N ILE* 1.3 74.9 + - - +
104N ARG* 3.9 5.5 + - - -
126N HIS* 4.0 16.6 - - + -
127N LYS 3.6 4.3 - - - -
128N TRP* 3.4 25.3 - - + +
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Residues in contact with ILE 67 (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 5.7 0.7 - - - -
65N VAL* 3.8 7.6 - - + +
66N ALA* 1.3 87.0 - - - +
68N ARG* 1.3 83.2 + - - +
97N ILE* 3.5 27.1 - - + -
100N ILE* 4.1 13.9 - - + -
101N ALA* 3.8 29.4 - - + +
104N ARG* 2.9 50.3 - - - +
126N HIS* 3.4 5.7 - - - -
127N LYS* 2.9 35.4 + - - +
129N HIS* 5.4 0.2 - - - +
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Residues in contact with ARG 68 (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 5.8 1.0 + - - -
1469A C 3.4 29.3 + - - +
1470A A 2.8 44.8 + - - -
67N ILE* 1.3 86.3 - - - +
69N LYS* 1.3 55.0 + - - +
70N GLY 3.3 18.4 + - - -
71N SER 3.6 17.4 + - - -
72N SER* 4.4 1.2 - - - +
73N ARG* 3.1 36.3 - - - +
93N ARG* 4.4 5.7 - - - +
97N ILE* 3.5 21.4 - - - +
100N ILE* 4.7 7.1 - - - +
104N ARG* 4.8 2.8 - - - +
125N ARG 3.4 8.5 - - - +
126N HIS* 4.7 0.9 - - - +
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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
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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