Contacts of the strand formed by residues 63 - 68 (chain A) in PDB entry 2P0K
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 63 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61A SER 3.7 7.8 + - - +
62A MET* 1.3 75.4 - - - +
64A LEU* 1.3 64.0 + - - +
77A ILE* 4.2 9.0 - - + -
78A ALA 3.3 5.4 - - - +
79A THR* 3.0 25.1 + - - +
93A ASP* 2.7 25.1 + - - +
113A ILE* 3.4 24.2 + - + +
143A THR* 3.6 34.5 - - + +
144A LEU* 4.4 2.9 - - + -
147A ALA* 3.7 21.5 - - + +
148A GLU 2.9 10.3 + - - +
150A ALA* 2.9 23.6 + - - +
305A CL 2.9 22.8 - - - +
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Residues in contact with LEU 64 (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 PHE* 4.5 12.6 - - + -
62A MET 4.0 1.8 - - - +
63A LYS* 1.3 78.8 - - - +
65A GLU* 1.3 83.4 + - - +
66A ALA* 4.3 0.2 - - + -
77A ILE* 3.5 8.8 - - - +
78A ALA* 2.9 43.8 + - + +
80A VAL* 3.7 29.4 - - + -
88A LEU* 4.8 0.7 - - + -
90A LEU* 4.0 11.2 - - + -
110A ILE* 3.8 29.2 - - + -
111A GLN 3.5 10.3 - - - +
113A ILE* 3.8 11.4 - - - +
150A ALA* 4.5 0.9 - - + -
155A PHE* 3.7 14.6 - - + -
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Residues in contact with GLU 65 (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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64A LEU* 1.3 79.2 - - - +
66A ALA* 1.3 61.7 + - - +
75A THR* 3.8 14.1 - - + +
76A CYS 3.3 3.4 - - - -
77A ILE* 4.2 7.8 - - + +
110A ILE* 3.3 4.0 - - - -
111A GLN* 2.7 48.3 + - - +
112A PRO 3.5 17.6 - - - +
113A ILE* 3.6 7.7 - - - +
114A GLY* 2.9 22.3 + - - -
115A ASN* 3.6 3.3 + - - +
116A CYS* 2.9 33.2 + - - +
117A GLU* 5.1 3.5 + - - +
123A LEU* 3.8 26.6 - - + +
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Residues in contact with ALA 66 (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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64A LEU* 4.2 0.4 + - + -
65A GLU* 1.3 76.4 - - - +
67A GLN* 1.3 68.7 + - - +
68A ASP* 3.5 0.5 + - - -
75A THR* 4.2 0.2 - - - +
76A CYS* 2.9 32.7 + - - +
78A ALA* 4.0 22.0 - - + -
90A LEU* 4.8 0.2 - - + -
92A LEU* 4.7 1.5 - - + +
101A PHE* 4.0 20.2 - - + -
109A GLU 3.4 13.5 - - - +
110A ILE* 4.1 11.4 - - + -
111A GLN* 4.5 1.1 - - - -
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Residues in contact with GLN 67 (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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66A ALA* 1.3 76.6 - - - +
68A ASP* 1.3 65.2 + - - +
69A PRO* 3.2 9.9 - - - +
72A THR* 3.4 32.4 - - + +
73A THR 5.2 0.9 - - - -
74A SER 3.2 8.1 - - - +
75A THR* 2.8 28.7 + - - +
101A PHE* 4.4 4.0 - - - -
103A ARG* 4.8 4.9 + - - -
108A ALA 4.2 0.5 - - - +
109A GLU* 3.2 28.6 + - + +
111A GLN* 2.8 40.8 + - - +
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Residues in contact with ASP 68 (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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66A ALA 3.5 3.0 + - - -
67A GLN* 1.3 69.7 - - - +
69A PRO* 1.4 71.7 - - - +
70A ARG* 2.8 23.7 + - - +
71A ASN* 3.0 38.2 + - + +
72A THR* 3.2 7.1 - - - +
74A SER* 3.1 9.2 + - - +
76A CYS* 3.7 16.5 - - - -
92A LEU* 3.5 17.8 - - + +
125A PRO 4.6 0.7 - - - +
126A PRO* 3.6 3.8 - - - +
127A LEU* 2.8 36.8 + - - +
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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