Contacts of the strand formed by residues 72 - 79 (chain B) in PDB entry 2PJY
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 ILE 72 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B PHE* 3.5 10.0 - - - +
36B SER* 3.3 37.3 + - - +
37B THR* 4.6 3.1 - - - -
38B CYS 3.6 16.2 - - - +
39B ASP* 3.6 26.5 - - + +
65B TRP* 3.4 35.0 - - + +
66B ARG 3.4 11.4 - - - +
67B LYS* 3.8 21.3 - - + +
71B ASN* 1.3 81.5 - - - +
73B THR* 1.3 73.3 + - - +
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Residues in contact with THR 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B VAL* 5.6 10.3 - - + -
34B ARG 3.4 12.1 - - - +
35B PHE* 3.8 30.1 - - + +
36B SER* 4.3 0.7 - - - +
64B VAL 3.7 0.7 - - - +
65B TRP* 3.7 2.4 - - - -
66B ARG* 2.8 58.4 + - - +
71B ASN* 4.9 3.1 + - - +
72B ILE* 1.3 84.3 - - - +
74B LEU* 1.3 61.3 + - - +
75B GLU 4.3 0.2 - - - -
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Residues in contact with LEU 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B ASP 3.1 2.9 - - - +
33B VAL* 4.7 0.7 - - - -
34B ARG* 2.6 39.5 + - + +
36B SER* 3.7 25.5 - - - +
38B CYS* 5.4 4.7 - - + -
44B CYS* 6.1 0.2 - - + -
45B MET 4.8 2.2 - - - +
46B SER* 4.1 26.7 - - - +
64B VAL 3.4 14.8 - - - +
65B TRP* 3.7 30.5 - - + -
73B THR* 1.3 75.0 - - - +
75B GLU* 1.3 63.2 + - - +
76B THR* 4.9 5.1 + - + -
100B MET* 5.0 1.8 - - + -
124B ILE* 3.7 35.2 - - + -
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Residues in contact with GLU 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B ASP* 3.3 21.5 - - - +
33B VAL* 3.8 18.8 + - + +
62B VAL 3.7 0.6 - - - +
63B ALA* 3.2 8.3 - - - +
64B VAL* 2.8 47.1 + - + +
66B ARG* 5.5 1.4 - - - -
74B LEU* 1.3 75.8 - - - +
76B THR* 1.3 66.3 + - - +
77B VAL* 3.7 9.4 - - + +
85B TYR* 2.6 34.3 + - - -
86B HIS* 2.7 31.5 + - - -
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Residues in contact with THR 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B LYS* 3.3 31.2 - - + -
30B PHE* 3.4 2.4 - - - -
31B CYS* 3.0 37.1 + - - +
32B ASP* 2.9 31.0 + - - +
46B SER* 4.4 12.3 - - - +
48B CYS* 3.8 4.0 - - + +
62B VAL 3.5 4.0 - - - +
63B ALA* 4.8 4.3 - - + -
74B LEU* 4.9 9.5 + - + -
75B GLU* 1.3 79.0 - - - +
77B VAL* 1.3 61.1 + - - +
121B ASN* 4.0 19.1 - - - +
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Residues in contact with VAL 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A ARG* 4.2 6.3 - - - +
28B CYS* 4.5 0.3 - - - +
29B LYS 3.4 9.4 + - - -
30B PHE* 3.5 22.2 - - + -
32B ASP* 3.7 11.2 - - - +
61B CYS* 3.7 3.8 - - - -
62B VAL* 2.9 41.0 + - + +
64B VAL* 5.8 0.4 - - + -
75B GLU* 3.7 21.8 - - + +
76B THR* 1.3 79.0 - - - +
78B CYS* 1.3 75.4 + - - +
79B HIS* 5.1 0.9 - - + -
85B TYR* 3.5 36.6 - - + +
121B ASN* 4.1 1.7 + - - -
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Residues in contact with CYS 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B CYS* 3.7 14.1 - - - -
30B PHE* 3.3 32.7 - - + -
52B SER 4.5 3.1 - - - -
53B ILE 4.8 0.4 - - - -
54B CYS* 2.0 60.1 - - + -
59B GLU* 3.7 16.8 - - - +
60B VAL 3.4 4.9 - - - -
77B VAL* 1.3 84.2 - - - +
79B HIS* 1.3 63.3 + - - +
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Residues in contact with HIS 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B GLU* 3.9 7.5 - - - +
60B VAL* 2.8 43.6 + - - +
62B VAL* 3.8 19.1 - - + -
77B VAL* 5.1 2.2 - - + -
78B CYS* 1.3 77.0 + - - +
80B ASP* 1.3 80.9 + - - +
83B LEU* 2.8 49.1 + - + -
84B PRO 3.8 4.2 + - - -
85B TYR* 3.5 44.3 - + + +
90B LEU* 3.6 14.1 - - + -
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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