Contacts of the strand formed by residues 51 - 58 (chain C) in PDB entry 1NPP
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 51 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50C ALA* 1.3 74.9 - - - +
52C GLU* 1.3 75.9 + - - +
53C LYS* 3.1 34.5 + - + +
67C SER* 3.0 28.1 + - - -
69C LYS* 5.4 2.3 + - - +
130C LEU* 3.6 2.3 - - - -
131C ASP 3.4 25.2 + - - +
134C ILE* 5.9 4.5 - - + +
184C ILE* 3.9 19.6 - - + +
187C GLY* 4.4 21.2 - - - +
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Residues in contact with GLU 52 (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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50C ALA 5.0 1.1 - - - +
51C GLU* 1.3 86.6 - - - +
53C LYS* 1.3 59.0 + - - +
68C LEU* 3.2 49.2 + - + +
69C LYS* 4.9 10.5 + - + +
111C SER 4.1 4.8 - - - +
112C LYS* 4.3 9.8 - - - +
113C PRO* 3.0 30.7 - - + +
128C ILE* 4.4 4.3 - - + -
129C VAL 3.4 6.1 - - - +
130C LEU* 3.4 18.3 - - + +
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Residues in contact with LYS 53 (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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51C GLU* 3.1 32.6 + - - +
52C GLU* 1.3 78.9 - - - +
54C VAL* 1.3 62.6 + - - +
55C VAL 4.1 0.2 - - - -
65C ARG* 3.7 31.5 + - + +
66C LEU 3.2 12.7 - - - +
67C SER* 4.5 10.9 - - - +
68C LEU* 4.2 1.3 - - - +
128C ILE* 3.1 8.8 - - - +
129C VAL* 2.6 51.1 + - + +
131C ASP* 3.7 29.4 - - + -
133C LYS* 5.2 7.2 - - - -
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Residues in contact with VAL 54 (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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53C LYS* 1.3 73.9 - - - +
55C VAL* 1.3 63.1 + - - +
56C ILE* 3.3 24.9 - - + +
64C TYR 3.6 0.7 - - - +
65C ARG* 3.3 3.8 - - - -
66C LEU 2.8 38.4 + - - +
68C LEU* 4.0 15.3 - - + -
88C ILE* 4.0 19.3 - - + -
93C VAL* 3.4 43.3 - - + -
126C ALA* 4.3 6.3 - - + -
127C LYS 3.4 4.9 - - - +
128C ILE* 3.6 13.0 - - + -
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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
----------------------------------------------------------
54C VAL* 1.3 75.0 - - - +
56C ILE* 1.3 63.9 + - - +
57C ARG* 3.2 33.9 - - + +
62C GLU* 3.2 16.2 - - + +
64C TYR 3.3 6.7 - - - +
65C ARG* 3.5 36.3 - - + +
125C GLU 3.7 0.7 - - - +
126C ALA* 3.3 3.6 - - - -
127C LYS* 2.6 49.6 + - - +
129C VAL* 3.6 22.9 - - + -
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Residues in contact with ILE 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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54C VAL* 3.3 34.5 - - + +
55C VAL* 1.3 80.9 - - - +
57C ARG* 1.3 64.3 + - - +
62C GLU* 3.7 2.6 - - - -
63C LYS* 2.8 25.3 + - - -
64C TYR* 2.8 29.7 + - + +
66C LEU* 5.2 2.7 - - + -
75C ILE* 4.6 10.8 - - + -
77C VAL* 3.9 28.9 - - + -
86C PHE* 3.8 41.3 - - + -
88C ILE* 5.2 5.6 - - + -
125C GLU 3.4 2.7 - - - +
126C ALA* 4.4 3.1 - - + -
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Residues in contact with ARG 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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55C VAL* 3.2 32.0 - - + +
56C ILE* 1.3 83.2 - - - +
58C ALA* 1.3 61.0 + - - +
59C GLN 4.2 0.2 - - - -
60C GLY* 3.4 29.4 + - - +
61C LYS 3.1 13.0 - - - +
62C GLU* 3.4 26.6 + - - +
63C LYS* 4.7 0.4 - - - -
65C ARG* 5.0 1.8 - - - +
77C VAL* 4.6 0.2 - - - +
124C THR* 3.3 6.0 - - - -
125C GLU* 2.8 50.1 + - + +
127C LYS* 4.4 16.5 - - - +
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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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57C ARG* 1.3 74.5 - - - +
59C GLN* 1.3 72.7 + - + +
60C GLY 3.2 0.2 - - - -
61C LYS* 2.9 23.4 + - - +
63C LYS* 4.0 24.0 - - + +
77C VAL* 4.3 7.6 - - + -
78C LEU 3.6 24.0 - - - +
79C GLY* 4.6 1.3 - - - -
123C LYS 3.6 4.3 - - - -
124C THR* 4.2 10.5 - - + -
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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