Contacts of the strand formed by residues 54 - 59 (chain A) in PDB entry 2YD6
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 LYS 54 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A ARG* 3.8 20.4 + - - +
53A PRO* 1.3 90.5 - - - +
55A ILE* 1.3 64.3 + - - +
56A VAL* 5.6 0.6 - - - +
73A GLU* 6.2 0.4 - - - -
76A ASP 3.3 20.6 + - - +
77A GLY* 3.6 19.5 - - - +
78A SER* 4.3 3.8 - - - -
99A VAL 3.6 1.0 - - - +
100A ALA* 3.5 1.2 - - - -
101A SER* 3.0 38.8 + - - +
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Residues in contact with ILE 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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45A CYS* 3.5 32.5 - - - +
46A GLN* 4.1 2.7 - - - -
47A ALA* 4.3 5.8 - - + +
54A LYS* 1.3 81.1 - - - +
56A VAL* 1.3 76.5 + - - +
57A TRP* 3.9 7.9 - - - +
71A VAL* 5.5 3.3 - - - +
73A GLU* 5.4 3.5 - - - +
77A GLY 3.8 7.3 + - - +
78A SER* 3.4 29.2 - - - +
80A SER* 3.6 29.1 + - - +
98A CYS* 3.5 23.1 - - - -
99A VAL 3.2 6.7 - - - +
100A ALA* 4.2 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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54A LYS 4.3 1.3 + - - +
55A ILE* 1.3 79.8 - - - +
57A TRP* 1.3 66.4 + - - +
58A ASN* 4.0 17.3 - - - +
63A LYS* 4.0 28.5 - - + +
71A VAL* 6.3 0.4 - - - -
98A CYS* 3.7 2.1 - - - -
99A VAL* 2.8 53.7 + - + +
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Residues in contact with TRP 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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30A PRO* 4.2 9.9 - - + -
43A PHE* 3.6 45.8 - + + -
44A ILE 4.2 0.7 - - - -
45A CYS* 3.6 31.0 - - + -
55A ILE* 3.9 6.0 - - + +
56A VAL* 1.3 79.0 - - - +
58A ASN* 1.3 65.4 + - - +
63A LYS* 3.5 4.9 - - - +
64A VAL* 2.9 40.8 + - + +
71A VAL* 3.8 22.8 - - + +
80A SER* 2.8 33.7 + - - -
82A LEU* 3.6 30.6 - - + +
96A TYR* 4.9 4.5 - - + -
97A GLU 3.2 18.2 - - - -
98A CYS* 3.8 15.3 - - + -
111A THR* 4.8 4.9 - - + -
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Residues in contact with ASN 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* 4.0 13.0 - - - +
57A TRP* 1.3 76.5 - - - +
59A LYS* 1.3 61.4 + - - +
60A LYS 5.1 0.2 - - - +
61A GLY* 4.1 20.0 + - - +
62A LYS 3.2 15.5 - - - +
63A LYS* 3.3 21.7 + - - +
64A VAL* 3.9 4.9 - - - -
96A TYR* 3.4 9.4 - - - +
97A GLU* 2.9 44.8 + - + +
99A VAL* 3.5 24.3 - - - +
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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 ASN* 1.3 74.1 - - - +
60A LYS* 1.3 91.3 + - + +
61A GLY 3.0 0.4 - - - -
62A LYS* 2.8 27.7 + - - +
64A VAL* 4.2 5.6 - - + +
91A ARG* 4.7 12.9 + - - +
94A ALA* 3.8 24.7 - - + +
95A ILE 3.8 15.9 - - - +
96A TYR* 3.9 21.7 + - + +
97A GLU* 6.3 0.4 - - - -
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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