Contacts of the strand formed by residues 51 - 58 (chain A) in PDB entry 1NPR
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50A ALA* 1.3 75.6 - - - +
52A GLU* 1.3 73.6 + - - +
53A LYS* 3.2 22.9 + - - +
67A SER* 3.2 21.1 + - - -
69A LYS* 6.2 0.3 - - - -
130A LEU* 3.5 4.6 - - - -
131A ASP* 2.8 40.6 + - - +
132A ASN* 2.7 30.1 + - - +
184A ILE* 3.7 14.0 - - + +
185A LYS* 3.7 24.3 - - + +
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Residues in contact with GLU 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A ALA 5.7 0.9 - - - +
51A GLU* 1.3 79.2 - - - +
53A LYS* 1.3 65.0 + - - +
67A SER* 3.7 0.5 - - - -
68A LEU* 3.1 49.7 + - + +
69A LYS 4.9 0.3 + - - -
111A SER 4.4 5.1 - - - +
113A PRO* 3.7 22.2 - - + +
128A ILE* 4.6 3.4 - - + -
129A VAL 3.4 8.3 - - - +
130A LEU* 3.6 16.8 - - + -
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Residues in contact with LYS 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A GLU* 3.2 36.9 + - + +
52A GLU* 1.3 82.4 - - - +
54A VAL* 1.3 64.3 + - - +
65A ARG* 4.0 31.4 + - + +
66A LEU 3.2 13.9 - - - +
67A SER* 4.0 11.2 - - - +
68A LEU* 4.0 1.8 - - - +
127A LYS 3.5 0.9 - - - +
128A ILE* 3.3 5.9 - - - -
129A VAL* 2.9 45.2 + - + +
131A ASP* 4.1 13.5 + - + +
132A ASN* 3.8 16.0 + - - +
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Residues in contact with VAL 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A LYS* 1.3 74.1 - - - +
55A VAL* 1.3 63.3 + - - +
56A ILE* 4.0 10.8 + - + +
64A TYR 3.7 1.4 - - - +
65A ARG* 3.2 4.7 - - - -
66A LEU* 2.6 40.0 + - + +
68A LEU* 3.5 35.2 - - + -
88A ILE* 3.8 28.7 - - + -
93A VAL* 3.6 18.4 - - + -
126A ALA* 4.1 24.9 - - + -
127A LYS 3.5 6.7 - - - +
128A ILE* 4.7 3.1 - - + -
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Residues in contact with VAL 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A LYS 4.9 0.2 - - - -
54A VAL* 1.3 77.3 - - - +
56A ILE* 1.3 62.8 + - - +
57A ARG* 4.0 14.5 + - + +
62A GLU* 3.6 28.5 - - + +
64A TYR 3.3 7.6 - - - +
65A ARG* 3.7 35.9 - - + +
125A GLU* 3.6 1.9 - - - +
126A ALA* 3.2 3.1 - - - -
127A LYS* 2.9 53.3 + - + +
129A VAL* 3.8 22.4 - - + -
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Residues in contact with ILE 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A VAL* 4.1 14.4 - - + +
55A VAL* 1.3 76.2 - - - +
57A ARG* 1.3 61.3 + - - +
62A GLU* 3.7 0.9 - - - +
63A LYS* 2.7 31.9 + - + -
64A TYR* 2.9 25.4 + - + +
66A LEU* 5.0 1.8 - - + -
75A ILE* 3.9 36.8 - - + -
77A VAL* 3.9 27.6 - - + -
86A PHE* 3.8 36.8 - - + -
88A ILE* 4.9 2.0 - - + -
125A GLU 3.3 3.4 - - - +
126A ALA* 3.9 15.3 - - + -
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Residues in contact with ARG 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A VAL* 4.2 12.8 - - + +
56A ILE* 1.3 84.4 - - - +
58A ALA* 1.3 62.8 + - - +
59A GLN 4.1 0.9 - - - -
60A GLY* 2.6 41.5 + - - +
61A LYS 3.1 10.6 - - - +
62A GLU* 4.1 10.6 - - - +
63A LYS* 4.7 0.7 - - - -
77A VAL* 4.9 0.2 - - - +
124A THR* 3.4 7.2 - - - -
125A GLU* 2.8 54.5 + - + +
127A LYS* 3.8 27.3 - - - +
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Residues in contact with ALA 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A ARG* 1.3 73.9 - - - +
59A GLN* 1.3 75.1 + - + +
61A LYS* 2.8 26.5 + - - +
63A LYS* 3.9 27.3 - - + +
77A VAL* 4.5 9.6 - - + -
78A LEU 3.7 24.5 - - - +
79A GLY* 4.8 0.4 - - - -
123A LYS 3.8 3.8 - - - -
124A THR* 4.6 4.5 - - + +
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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