Contacts of the strand formed by residues 68 - 75 (chain L) 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 VAL 68 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1993A C 3.7 38.6 - - - +
2596A A 4.6 17.9 - - - +
2597A U 5.7 0.2 - - - +
32L ILE* 4.5 3.4 - - + -
54L THR* 3.9 21.3 - - + -
55L VAL 3.2 9.9 - - - +
56L SER* 4.4 4.7 - - - -
66L ARG 3.7 3.6 + - - +
67L GLN* 1.3 75.1 - - - +
69L LEU* 1.3 68.4 + - - +
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Residues in contact with LEU 69 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29L LEU* 6.5 0.4 - - + -
54L THR* 3.6 6.2 - - - +
55L VAL* 2.7 42.5 + - + +
57L VAL* 4.2 13.7 - - + -
64L MET* 4.0 16.6 - - + -
67L GLN* 3.6 30.7 + - + +
68L VAL* 1.3 84.6 - - - +
70L GLU* 1.3 59.2 + - - +
97L ILE* 3.9 41.1 - - + -
98L VAL 5.3 0.2 - - - +
105L ARG* 4.5 12.8 - - - +
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Residues in contact with GLU 70 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2597A U 4.7 6.2 + - - -
35L HIS* 5.2 5.0 + - - +
52L LYS* 4.0 32.9 + - + +
53L ILE 3.7 11.4 - - - +
54L THR* 4.6 10.4 + - - +
69L LEU* 1.3 76.7 - - - +
71L ALA* 1.3 66.1 + - - +
97L ILE* 3.4 7.1 - - - +
98L VAL* 2.8 36.8 + - + +
99L ASP 3.8 18.1 - - - +
100L GLU* 4.7 5.2 - - - +
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Residues in contact with ALA 71 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29L LEU* 4.8 3.1 - - + -
52L LYS* 3.3 10.0 - - - +
53L ILE* 2.9 32.4 + - + -
55L VAL* 4.1 21.3 - - + -
70L GLU* 1.3 78.4 - - - +
72L VAL* 1.3 64.9 + - - +
95L ALA* 4.3 11.9 - - + -
96L VAL 3.3 19.7 - - - +
97L ILE* 3.9 7.6 - - + +
98L VAL* 3.9 3.3 - - - +
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Residues in contact with VAL 72 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50L GLY 4.7 1.6 - - - -
51L ASP 3.5 6.1 - - - +
52L LYS* 4.5 8.1 - - + -
71L ALA* 1.3 82.5 - - - +
73L VAL* 1.3 74.6 + - - +
74L VAL* 3.3 6.4 + - + +
95L ALA* 3.0 6.3 - - - -
96L VAL* 2.9 33.0 + - + +
98L VAL* 4.6 18.2 - - + -
102L GLU* 6.0 0.2 - - + -
117L VAL* 4.1 9.2 - - + -
121L PHE* 3.3 56.3 - - + -
124L VAL* 5.1 6.7 - - + -
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Residues in contact with VAL 73 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12L LEU* 4.3 21.1 - - + -
18L ILE* 5.1 0.2 - - + -
47L ALA* 5.0 0.2 - - + -
48L GLY* 3.3 36.3 - - - +
49L LEU* 3.3 8.0 - - - +
50L GLY* 3.0 24.3 + - - -
51L ASP* 3.1 12.8 + - + +
53L ILE* 3.9 32.5 - - + -
72L VAL* 1.3 76.2 - - - +
74L VAL* 1.3 62.2 + - - +
75L ARG 4.0 14.1 - - - +
76L GLN* 4.9 1.8 - - + +
94L ALA 3.7 11.7 - - - +
95L ALA* 4.1 3.1 - - + -
117L VAL* 4.1 1.6 - - - +
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Residues in contact with VAL 74 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21L ALA* 5.6 2.7 - - + -
49L LEU* 3.1 19.3 - - - +
72L VAL* 3.3 9.6 + - + +
73L VAL* 1.3 74.9 - - - +
75L ARG* 1.3 63.5 + - + +
94L ALA* 2.8 14.9 + - + +
96L VAL* 3.7 28.9 - - + -
112L PRO 3.7 5.4 - - - +
113L ILE* 3.1 51.6 - - + -
114L ALA* 3.6 11.6 + - - +
117L VAL* 4.2 13.0 - - + +
124L VAL* 4.7 4.9 - - + -
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Residues in contact with ARG 75 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19L THR* 4.8 4.2 - - - +
21L ALA* 3.4 18.6 - - - +
49L LEU* 3.9 3.3 - - - +
73L VAL* 3.7 8.0 - - - +
74L VAL* 1.3 87.3 - - + +
76L GLN* 1.3 64.6 + - - +
90L PHE* 3.3 33.4 - - + -
91L GLU* 5.3 3.0 + - - +
92L ASP* 3.2 36.9 + - - +
93L ASN* 3.1 2.9 - - - +
94L ALA* 2.7 55.9 + - - +
110L LYS 3.6 7.2 + - - -
111L GLY* 4.0 4.6 - - - -
112L PRO* 3.3 46.1 + - - +
24V LYS* 4.5 9.1 + - - +
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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