Contacts of the strand formed by residues 55 - 60 (chain C) in PDB entry 1NAP
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 GLU 55 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64A ARG* 6.1 1.2 - - - -
65A LYS 5.5 2.4 + - - -
25C CYS* 3.3 14.5 - - - +
26C LEU* 2.6 42.1 + - - +
27C CYS* 2.8 32.9 + - + +
43C GLU 3.5 1.9 - - - +
44C VAL* 3.5 2.8 - - - -
45C ILE* 2.9 58.0 + - + +
51C CYS* 4.1 8.7 - - + +
53C GLN* 3.9 10.5 - - + +
54C VAL* 1.3 78.6 - - - +
56C VAL* 1.3 63.7 + - - +
57C ILE* 4.0 2.9 - - + -
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Residues in contact with VAL 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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27C CYS* 4.8 1.4 - - - -
42C LEU* 4.7 11.9 - - + -
43C GLU 3.3 7.0 - - - +
44C VAL* 4.2 13.2 - - + -
54C VAL* 4.2 3.6 - - + -
55C GLU* 1.3 78.9 - - - +
57C ILE* 1.3 66.6 + - - +
67C CYS* 3.3 6.2 - - - +
68C LEU* 2.9 66.3 + - + +
70C PRO* 3.9 18.2 - - + -
75C ILE* 5.0 3.4 - - + -
79C VAL* 5.5 1.8 - - + -
83D LEU* 3.4 31.4 - - + -
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Residues in contact with ILE 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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26A LEU* 4.4 6.3 - - + -
65A LYS* 3.9 20.4 - - + -
26C LEU* 2.9 39.7 - - + -
27C CYS* 4.0 14.8 - - - -
42C LEU* 3.4 2.0 - - - -
43C GLU* 2.8 49.4 + - + +
45C ILE* 4.1 12.8 - - + -
55C GLU* 4.7 1.1 - - + -
56C VAL* 1.3 82.0 - - - +
58C ALA* 1.3 61.7 + - - +
59C THR* 4.1 2.3 + - - +
65C LYS* 3.9 34.1 - - + +
66C ILE 3.4 6.3 - - - +
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Residues in contact with ALA 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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39C ILE* 4.4 5.8 - - + -
41C SER 3.4 6.1 - - - +
42C LEU* 3.8 22.0 - - + -
56C VAL 4.0 1.4 + - - -
57C ILE* 1.3 74.8 - - - +
59C THR* 1.3 61.0 + - - +
60C LEU* 3.9 8.7 + - + -
65C LYS* 3.2 8.1 - - - +
66C ILE* 2.9 51.3 + - + +
68C LEU* 4.1 11.2 - - + -
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Residues in contact with THR 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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39C ILE* 3.7 2.9 - - - -
40C GLN* 2.9 40.8 + - - +
41C SER* 2.7 31.2 + - - +
57C ILE* 4.1 2.5 + - - +
58C ALA* 1.3 71.7 - - - +
60C LEU* 1.3 69.8 + - - +
63C GLY* 4.4 9.9 - - - +
64C ARG 3.6 8.1 - - - +
65C LYS* 3.0 34.1 + - + +
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Residues in contact with LEU 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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24A ARG* 4.6 11.0 - - - +
34C ILE* 3.8 26.2 - - + -
38C ASN* 3.1 24.9 - - + +
39C ILE* 4.1 6.1 - - + -
40C GLN* 3.0 11.9 + - - -
58C ALA* 4.3 2.2 - - + -
59C THR* 1.3 80.0 - - - +
61C LYS* 1.3 56.8 + - - +
62C ASP* 2.9 18.8 - - - +
63C GLY* 2.7 24.9 + - - -
64C ARG* 2.9 30.2 + - + +
66C ILE* 3.9 36.1 - - + -
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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