Contacts of the strand formed by residues 65 - 76 (chain R) in PDB entry 4PJO
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 MET 65 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3Q LEU* 4.3 3.1 - - - -
32R LEU* 4.5 21.5 - - + -
42R VAL* 4.3 2.9 - - + -
44R ILE* 3.6 26.0 - - + -
56R VAL* 3.6 24.7 - - + -
58R ALA 3.3 5.8 - - - +
59R PHE* 3.9 15.5 - - + -
63R CYS* 3.2 13.2 + - - +
64R ASN* 1.3 78.7 - - - +
66R VAL* 1.3 61.9 + - - +
67R LEU* 3.5 33.6 + - + -
100R PHE* 3.4 5.6 - - - -
101R LEU* 2.8 38.9 + - + +
106R VAL* 4.8 6.5 - - - -
109R VAL* 4.7 8.1 - - + -
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Residues in contact with VAL 66 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3Q LEU* 4.2 8.9 - - + +
6Q PHE* 4.2 20.0 - - + -
70Q LEU* 5.3 1.3 - - + -
76Q LEU* 4.2 26.7 - - + -
80Q LEU* 4.6 12.1 - - + -
56R VAL* 3.7 0.7 - - - -
57R LYS* 2.9 41.9 + - + -
58R ALA* 3.0 17.8 + - + +
65R MET* 1.3 73.4 - - - +
67R LEU* 1.3 69.0 + - - +
99R MET 3.3 11.0 - - - +
100R PHE* 3.9 24.2 - - + -
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Residues in contact with LEU 67 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42R VAL* 4.9 2.7 - - + -
44R ILE* 4.0 20.9 - - + -
52R LEU* 4.2 17.3 - - + -
54R GLY* 5.1 2.5 - - - +
55R ARG 3.2 17.3 - - - +
56R VAL* 3.9 5.6 - - + -
57R LYS* 5.1 0.7 - - - -
65R MET* 3.5 33.4 - - + +
66R VAL* 1.3 83.2 - - - +
68R GLU* 1.3 64.9 + - - +
70R VAL* 3.4 22.4 - - + -
98R LYS* 3.4 5.2 - - - +
99R MET* 2.9 49.3 + - + +
101R LEU* 4.5 9.2 - - + -
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Residues in contact with GLU 68 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76Q LEU* 3.8 20.3 - - + +
54R GLY* 3.8 0.7 - - - -
55R ARG* 2.9 36.5 + - + +
57R LYS* 3.3 44.6 + - + +
67R LEU* 1.3 73.7 - - - +
69R ASN* 1.3 89.8 + - - +
70R VAL* 3.2 4.3 + - - -
97R SER 3.2 9.6 - - - +
98R LYS* 4.1 14.6 - - + -
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Residues in contact with ASN 69 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41R GLN* 5.6 2.9 + - - -
53R LEU 3.6 8.0 - - - +
54R GLY* 3.7 4.3 - - - -
55R ARG* 4.3 22.4 - - + +
68R GLU* 1.3 95.1 + - - +
70R VAL* 1.3 63.1 + - - +
71R LYS* 5.2 0.7 - - - +
95R TYR* 3.0 36.0 + - + -
96R ILE 3.8 1.1 - - - -
97R SER* 2.9 13.7 + - - +
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Residues in contact with VAL 70 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52R LEU* 3.8 28.5 - - + -
53R LEU 3.3 9.6 - - - +
54R GLY* 4.1 4.0 - - - +
67R LEU* 3.4 36.1 - - + +
68R GLU 3.8 9.4 - - - +
69R ASN* 1.3 75.7 - - - +
71R LYS* 1.3 67.8 + - - +
72R GLU* 4.0 2.2 - - - +
95R TYR* 3.3 10.4 - - - -
96R ILE* 2.8 37.2 + - + +
99R MET* 3.5 31.0 - - + +
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Residues in contact with LYS 71 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47N GLU* 3.4 28.5 + - + +
51R LYS 3.4 2.8 - - - +
53R LEU* 2.9 37.9 + - + +
69R ASN 5.2 1.1 - - - +
70R VAL* 1.3 75.6 - - - +
72R GLU* 1.3 64.2 + - - +
73R MET* 3.8 30.7 - - + +
93R ASP* 4.0 26.2 + - + +
94R ARG 3.4 9.6 - - - +
95R TYR* 4.5 5.2 - - + +
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Residues in contact with GLU 72 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67Q TYR* 2.4 33.0 + - - -
48R ASN* 4.1 1.4 + - - -
50R LYS* 3.2 27.9 + - + +
51R LYS 3.3 4.7 - - - -
52R LEU* 4.0 18.9 - - + +
70R VAL* 4.0 3.1 - - + +
71R LYS* 1.3 74.2 - - - +
73R MET* 1.3 61.7 + - - +
74R TRP* 3.5 13.7 - - + -
93R ASP* 3.1 5.7 - - - +
94R ARG* 2.5 73.8 + - + +
96R ILE* 4.6 10.7 - - + +
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Residues in contact with MET 73 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44N TYR* 3.8 33.4 - - + -
47N GLU* 3.5 33.7 - - + -
43R LEU* 4.1 12.8 - - + -
50R LYS* 3.6 0.7 - - - -
51R LYS* 2.7 42.3 + - + +
53R LEU* 3.8 29.8 - - + -
71R LYS* 3.8 31.9 - - + +
72R GLU* 1.3 81.2 - - - +
74R TRP* 1.3 65.3 + - - +
92R LYS 3.3 7.6 - - - +
93R ASP* 4.2 4.3 - - + -
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Residues in contact with TRP 74 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44N TYR* 4.1 11.5 + - - -
49R ASN 4.4 5.4 - - - +
50R LYS* 3.6 44.2 - - + +
51R LYS* 5.5 1.1 - - - +
72R GLU* 3.5 40.2 - - + -
73R MET* 1.3 83.4 - - - +
75R THR* 1.3 77.2 + - - +
76R GLU* 3.2 34.6 + - + +
91R ASN* 3.8 4.2 - - - +
92R LYS* 2.9 47.8 + - + +
93R ASP* 3.8 13.7 - - - -
94R ARG* 3.8 25.1 - - + -
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Residues in contact with THR 75 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36N GLN* 2.9 26.1 + - + +
39N CYS* 5.4 11.9 - - - -
44N TYR* 4.6 8.8 + - - +
49R ASN* 5.6 5.3 + - - +
74R TRP* 1.3 86.2 + - - +
76R GLU* 1.3 63.1 + - - +
89R PRO* 4.7 13.4 - - + +
90R VAL 3.3 13.7 + - - -
91R ASN* 3.8 11.8 + - - -
92R LYS 4.8 0.2 - - - +
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Residues in contact with GLU 76 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36N GLN* 4.4 6.5 - - - +
74R TRP* 3.2 31.5 + - + +
75R THR* 1.3 78.0 - - - +
77R VAL* 1.3 61.8 + - - +
89R PRO* 3.4 7.3 - - - +
90R VAL* 2.8 38.7 + - + +
92R LYS* 3.6 37.1 + - + +
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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