Contacts of the strand formed by residues 54 - 60 (chain C) 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 PRO 54 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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521 THR 3.7 14.1 - - - +
531 GLY* 3.7 22.4 - - - +
541 ILE* 3.9 22.2 - - + -
651 ALA* 4.9 8.7 - - + -
661 GLY 4.8 0.7 - - - +
45C ILE* 4.2 8.1 - - + -
46C GLU 3.2 11.0 - - - +
47C HIS* 4.5 1.1 - - - -
51C ARG* 3.7 13.7 + - - -
53C ALA* 1.3 92.6 - - + +
55C VAL* 1.3 61.1 + - - +
70C ALA* 4.1 11.3 + - + +
159C VAL* 6.0 0.2 - - - +
160C GLY* 4.3 8.9 - - - -
161C GLY* 4.1 19.1 - - - +
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Residues in contact with VAL 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C LYS* 5.6 0.7 - - + -
27C LEU* 3.6 33.7 - - + -
45C ILE* 3.5 2.9 - - - -
46C GLU* 2.5 51.3 + - + +
47C HIS 5.3 0.9 - - - +
48C ASP* 4.3 16.8 - - + +
51C ARG* 4.6 0.9 - - - +
54C PRO* 1.3 78.7 - - - +
56C ALA* 1.3 58.5 + - - +
67C LEU* 3.7 35.2 - - + -
68C ILE 2.8 23.6 - - - +
69C LEU* 4.1 2.7 - - - -
70C ALA* 3.9 4.5 - - - -
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Residues in contact with ALA 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C VAL* 4.4 10.1 - - + -
44C ASP 3.6 4.0 - - - +
45C ILE* 3.8 19.3 - - + -
55C VAL* 1.3 73.4 - - - +
57C ALA* 1.3 62.6 + - - +
58C VAL* 3.6 6.4 + - + -
67C LEU* 3.3 3.7 - - - -
68C ILE* 2.6 52.7 + - + +
70C ALA* 3.6 15.2 - - + +
74C VAL* 4.6 8.3 - - + -
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Residues in contact with ALA 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C VAL* 3.5 4.3 - - - -
43C VAL 2.7 32.1 + - - -
44C ASP* 2.7 28.1 + - + +
46C GLU* 4.0 8.3 - - - +
55C VAL 4.0 0.6 + - - -
56C ALA* 1.3 70.7 - - - +
58C VAL* 1.3 55.7 + - - +
65C ARG* 3.7 29.6 - - - +
66C ARG 4.0 1.3 - - - -
67C LEU* 3.5 21.6 - - + +
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Residues in contact with VAL 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C GLY* 4.0 4.5 - - - -
41C THR 3.5 20.4 - - - +
42C VAL* 4.3 10.5 - - + +
43C VAL* 4.9 0.4 - - - -
56C ALA* 4.1 10.5 - - + +
57C ALA* 1.3 79.5 - - - +
59C GLU* 1.3 64.0 + - - +
60C PHE* 3.5 32.9 - - + -
64C ASP 3.7 1.2 - - - +
65C ARG* 3.3 9.5 - - - +
66C ARG 3.0 35.6 + - - +
68C ILE* 4.2 12.6 - - + -
80C LEU* 4.0 27.8 - - + -
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Residues in contact with GLU 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C GLY* 3.0 1.7 - - - -
41C THR* 2.8 38.7 + - - +
43C VAL* 3.6 28.9 - - + +
58C VAL* 1.3 73.2 - - - +
60C PHE* 1.3 63.6 + - - +
61C GLU 4.1 0.2 + - - -
63C GLY* 5.4 7.2 - - - +
64C ASP 3.6 3.1 - - - +
65C ARG* 4.0 25.9 + - + +
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Residues in contact with PHE 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C ARG* 3.2 48.2 - - + +
38C ILE* 3.5 31.0 - - + -
39C ALA* 3.6 11.9 - - - -
40C GLY 3.9 9.0 - - - -
58C VAL* 3.5 29.6 - - + -
59C GLU* 1.3 77.7 - - - +
61C GLU* 1.3 66.5 + - - +
62C ASP* 3.2 3.6 - - - +
63C GLY* 2.9 18.0 + - - -
64C ASP* 2.7 24.4 + - + +
66C ARG* 4.5 12.8 - - + -
68C ILE* 4.1 19.1 - - + -
80C LEU* 5.1 4.3 - - + -
82C VAL* 4.4 15.9 - - + -
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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