Contacts of the strand formed by residues 26 - 34 (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 ALA 26 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20L CYS* 3.0 29.0 - - - +
22L ASP* 4.2 5.0 - - - +
24L THR* 3.3 14.2 + - - +
25L GLY* 1.3 80.2 + - - +
27L ARG* 1.3 61.7 + - - +
29L LEU* 4.3 2.7 - - + -
57L VAL* 3.9 25.8 - - + -
59L LYS 3.7 4.5 - - - -
64L MET* 4.0 6.5 - - + -
97L ILE* 3.8 18.6 - - + -
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Residues in contact with ARG 27 (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* 3.8 8.7 - - - +
20L CYS* 2.9 26.2 + - - +
25L GLY 4.7 3.1 - - - +
26L ALA* 1.3 75.9 - - - +
28L GLU* 1.3 57.3 + - + +
59L LYS* 2.8 24.1 + - + +
60L GLY* 4.1 16.2 - - - +
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Residues in contact with GLU 28 (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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17L LEU* 3.5 32.3 - - + +
18L ILE 3.6 9.1 - - - +
19L THR* 5.0 0.2 - - - +
27L ARG* 1.3 79.5 - - + +
29L LEU* 1.3 69.6 + - - +
57L VAL* 3.7 4.7 - - - +
58L THR* 2.8 56.8 + - - +
59L LYS* 3.2 46.4 + - + +
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Residues in contact with LEU 29 (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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16L SER 3.7 0.3 - - - +
17L LEU* 3.3 6.4 - - - +
18L ILE* 2.7 50.4 + - + +
19L THR 4.4 1.1 - - - +
20L CYS* 3.7 32.3 - - + -
26L ALA* 4.3 5.8 - - + -
28L GLU* 1.3 77.1 - - - +
30L LYS* 1.3 59.1 + - - +
31L VAL 4.1 0.2 - - - -
55L VAL* 3.2 24.7 - - + -
56L SER 3.6 1.1 - - - -
57L VAL* 3.7 29.6 - - + -
58L THR* 4.5 0.2 - - - -
69L LEU* 6.0 0.4 - - + -
71L ALA* 4.8 4.9 - - + -
95L ALA* 4.1 24.5 - - + +
97L ILE* 4.3 20.9 - - + -
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Residues in contact with LYS 30 (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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1992A U 3.2 15.0 + - - -
1993A C 2.6 51.5 + - + +
15L GLY* 4.2 11.0 - - - +
16L SER 3.3 7.0 - - - +
17L LEU* 3.4 21.3 - - + -
29L LEU* 1.3 74.2 - - - +
31L VAL* 1.3 74.3 + - - +
32L ILE* 3.5 2.5 + - + +
55L VAL* 3.0 15.2 - - - +
56L SER* 2.9 24.9 + - - +
58L THR* 3.6 15.9 + - - +
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Residues in contact with VAL 31 (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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1993A C 5.0 1.0 + - - -
12L LEU* 4.5 10.5 - - + -
13L GLU 3.6 24.7 - - - +
14L LYS* 4.2 6.4 - - - +
15L GLY* 2.8 25.7 + - - -
16L SER* 2.9 21.4 + - - +
18L ILE* 4.4 15.0 - - + -
29L LEU 4.1 0.2 - - - -
30L LYS* 1.3 74.0 - - - +
32L ILE* 1.3 65.8 + - - +
33L SER 4.0 20.0 - - - +
34L VAL* 5.0 1.8 - - + -
47L ALA* 4.9 7.6 - - + -
53L ILE* 3.9 27.1 - - + -
54L THR 3.9 3.8 - - - -
55L VAL* 4.5 2.2 - - + -
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Residues in contact with ILE 32 (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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1993A C 3.4 66.6 - - + +
2596A A 3.4 25.8 - - - +
14L LYS* 2.7 41.1 + - - +
30L LYS* 3.8 8.3 - - + +
31L VAL* 1.3 82.3 - - - +
33L SER* 1.3 60.9 + - - +
54L THR* 2.9 11.4 + - + +
55L VAL 4.0 4.9 - - - +
56L SER* 3.5 25.8 - - - +
68L VAL* 4.5 9.0 - - + -
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Residues in contact with SER 33 (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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2596A A 2.5 32.5 + - - +
2597A U 3.2 28.6 + - - -
8512A CL 3.3 14.5 - - - +
14L LYS* 5.4 1.3 - - - -
31L VAL* 4.0 3.6 - - - +
32L ILE* 1.3 86.4 + - - +
34L VAL* 1.3 63.6 + - - +
45L PRO* 5.8 0.9 - - - -
53L ILE* 3.1 10.6 - - - +
54L THR* 2.8 31.0 + - - +
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Residues in contact with VAL 34 (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 3.0 18.8 + - - -
14L LYS* 6.1 0.4 - - - +
31L VAL* 5.0 3.6 - - + -
33L SER* 1.3 78.9 - - - +
35L HIS* 1.3 72.8 + - - +
37L TYR* 3.1 32.0 + - + +
45L PRO* 4.8 8.5 - - + +
46L LYS 3.2 33.7 - - - +
47L ALA* 3.3 18.8 - - + -
51L ASP* 4.3 28.3 - - + +
52L LYS 4.0 2.7 - - - +
53L ILE* 4.3 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