Contacts of the strand formed by residues 51 - 60 (chain A) in PDB entry 3N51
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 TYR 51 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47A PHE* 3.0 48.3 + + + -
48A SER* 3.5 21.1 - - - +
49A ASP 3.8 0.2 - - - -
50A ARG* 1.3 103.4 + - + +
52A LYS* 1.3 59.7 + - - +
53A GLY 4.2 0.6 + - - -
68A CYS* 4.2 4.9 - - + -
69A LYS 3.4 3.1 - - - +
70A ASP* 3.9 28.2 + - + -
71A LYS* 3.7 5.5 + - - -
75A GLN* 5.2 1.1 - - + -
77A CYS* 3.4 31.2 - - - -
115A TYR* 5.2 3.3 - - - +
116A GLU* 2.7 30.4 + - - +
118A PHE* 3.8 13.5 - + - -
127A VAL* 3.8 17.8 - - + +
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Residues in contact with LYS 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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51A TYR* 1.3 73.9 - - - +
53A GLY* 1.3 70.3 + - - +
54A GLN* 3.6 11.5 + - + +
68A CYS* 3.2 4.1 - - - -
69A LYS* 2.9 62.8 + - + +
70A ASP 5.7 0.2 - - - -
71A LYS* 3.3 32.7 - - + +
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Residues in contact with GLY 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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47A PHE* 5.5 3.0 - - - -
51A TYR 4.2 1.0 + - - -
52A LYS* 1.3 80.8 - - - +
54A GLN* 1.3 62.0 + - - +
66A ILE* 4.0 8.5 - - - -
67A LEU 3.9 0.4 - - - -
68A CYS* 3.7 19.2 - - - -
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Residues in contact with GLN 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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52A LYS* 4.0 20.8 + - + +
53A GLY* 1.3 78.1 - - - +
55A ARG* 1.3 70.9 + - + +
66A ILE* 4.4 0.2 - - - +
67A LEU* 2.8 31.4 + - + +
68A CYS 4.6 0.6 + - - -
69A LYS* 3.3 40.1 + - + +
76A GLU* 3.6 27.1 + - - +
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Residues in contact with ARG 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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54A GLN* 1.3 87.9 - - - +
56A VAL* 1.3 65.7 + - - +
57A LEU* 5.3 6.1 - - + +
66A ILE* 3.7 5.7 - - - +
67A LEU* 2.8 68.5 + - + +
76A GLU* 4.3 10.5 + - - -
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Residues in contact with VAL 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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55A ARG* 1.3 80.9 - - - +
57A LEU* 1.3 65.8 + - - +
58A GLY* 3.6 16.8 - - - +
64A GLU* 4.3 27.6 - - + +
65A VAL 3.7 9.4 - - - +
66A ILE* 4.4 8.1 - - + +
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Residues in contact with LEU 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 ARG* 3.7 6.5 + - + +
56A VAL* 1.3 76.0 - - - +
58A GLY* 1.3 57.6 + - - +
65A VAL* 2.8 22.8 + - + +
66A ILE 3.9 3.6 - - - -
67A LEU* 3.5 47.1 - - + +
78A ALA* 3.9 12.6 - - + -
130A VAL* 3.8 26.7 - - + -
701A BK3 3.6 30.4 + - + +
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Residues in contact with GLY 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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56A VAL* 3.6 12.4 - - - +
57A LEU* 1.3 80.5 - - - +
59A LYS* 1.3 62.6 + - - -
64A GLU* 3.9 5.0 - - - +
65A VAL* 2.8 30.4 + - - +
701A BK3 4.4 7.0 - - - -
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Residues in contact with LYS 59 (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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58A GLY* 1.3 74.0 - - - -
60A GLY* 1.3 67.1 + - - +
62A PHE 4.3 3.6 - - - +
63A GLY* 3.5 37.4 - - - +
64A GLU* 4.5 8.5 - - + +
65A VAL* 4.9 0.4 - - - -
86A GLN* 4.6 17.9 + - - +
178A GLU* 4.6 9.2 - - - +
209A LYS* 5.6 6.7 - - + +
210A ASP* 4.0 26.8 + - - +
345A LEU* 5.9 8.1 - - + -
701A BK3 4.3 11.7 + - - +
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Residues in contact with GLY 60 (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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58A GLY 4.0 1.4 + - - -
59A LYS* 1.3 86.2 + - - +
61A SER* 1.3 67.3 + - - -
62A PHE 3.4 2.1 + - - -
63A GLY 3.2 18.1 + - - +
65A VAL* 4.2 9.0 - - - +
80A LYS* 4.3 6.7 - - - -
178A GLU* 5.3 5.4 - - - -
194A ILE* 6.3 1.1 - - - -
701A BK3 5.0 12.6 - - - -
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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