Contacts of the strand formed by residues 70 - 77 (chain W) in PDB entry 2JA7
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 ARG 70 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16W GLU* 4.7 5.5 + - - -
20W LYS* 5.6 0.8 - - - +
34W THR* 4.8 8.2 - - + +
35W PHE 2.9 17.3 - - - +
36W GLU* 3.0 40.8 + - - +
37W LYS* 5.4 2.7 - - - +
38W GLU 3.0 11.2 + - - +
39W ASP* 5.3 0.4 - - - +
63W VAL* 3.9 16.5 - - - +
64W GLU* 4.3 23.9 + - + -
65W HIS 6.3 0.4 - - - +
68W PHE* 3.0 55.9 + - + +
69W ALA* 1.3 78.2 - - - +
71W PHE* 1.3 69.1 + - - +
72W LYS* 6.4 0.9 - - - -
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Residues in contact with PHE 71 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33W ILE 3.5 0.2 - - - +
34W THR* 3.3 3.0 - - - -
35W PHE* 2.6 91.0 + + + -
38W GLU* 3.8 4.5 - - + -
39W ASP* 3.2 48.7 - - - -
42W LEU* 4.2 4.5 - - + -
43W GLY* 3.2 25.1 - - - -
46W ILE* 5.1 0.9 - - + -
61W TYR* 4.0 15.0 - + + -
62W LYS 3.1 22.2 - - - +
63W VAL* 4.2 5.6 - - + +
64W GLU* 5.0 2.0 - - - +
70W ARG* 1.3 79.2 - - - +
72W LYS* 1.3 69.1 + - - +
73W LEU* 4.3 6.3 - - + -
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Residues in contact with LYS 72 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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551M TYR* 3.5 27.5 - - + +
22W ASP* 6.1 0.9 - - - -
32W VAL* 4.0 14.5 - - + +
33W ILE 3.4 2.7 - - - -
34W THR* 3.3 26.9 - - + +
61W TYR* 3.3 3.8 - - - +
62W LYS* 3.0 37.6 + - + +
64W GLU* 3.4 35.0 + - + +
70W ARG* 6.4 1.3 - - - -
71W PHE* 1.3 77.0 - - - +
73W LEU* 1.3 60.8 + - - +
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Residues in contact with LEU 73 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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551M TYR* 4.6 1.1 - - - -
31W VAL 3.6 0.9 - - - +
32W VAL* 3.3 2.8 - - - -
33W ILE* 2.7 39.7 + - + +
35W PHE* 3.6 35.9 - - + -
43W GLY 5.6 0.9 - - - +
46W ILE* 4.1 17.7 - - + +
47W ARG* 4.3 10.5 - - + -
50W LEU* 3.9 14.8 - - + -
59W ALA 5.0 0.4 - - - -
60W ALA 2.9 29.6 - - - +
61W TYR* 3.7 11.4 - - + -
71W PHE* 4.3 5.8 - - + -
72W LYS* 1.3 74.1 - - - +
74W ARG* 1.3 66.0 + - - +
75W ILE* 3.7 27.7 + - + +
87W LEU* 4.3 0.9 - - + -
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Residues in contact with ARG 74 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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551M TYR* 3.8 37.6 - - + +
556M TRP* 3.5 29.5 - - - -
558M GLY* 4.2 11.5 + - - -
24W ASP* 3.0 35.8 + - - -
26W LYS* 5.0 3.0 - - - +
27W ALA* 4.7 7.3 - - - +
30W ALA* 3.9 15.5 - - - +
31W VAL 3.0 15.7 - - - +
32W VAL* 4.5 3.4 - - + -
58W PHE* 2.9 33.2 - - + -
59W ALA* 3.1 24.9 - - - +
60W ALA 3.0 12.4 + - - +
72W LYS 4.2 0.4 - - - -
73W LEU* 1.3 72.7 - - - +
75W ILE* 1.3 66.2 + - - +
76W GLN* 3.9 15.8 - - - +
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Residues in contact with ILE 75 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30W ALA* 3.0 5.0 - - - -
31W VAL* 2.7 42.2 + - + +
33W ILE* 4.0 23.6 - - + -
50W LEU* 3.4 47.3 - - + -
56W VAL* 4.5 0.7 - - + -
58W PHE 3.4 5.6 - - - +
73W LEU* 3.7 20.4 - - + +
74W ARG* 1.3 80.8 - - - +
76W GLN* 1.3 61.5 + - - +
77W THR* 4.5 7.9 - - + -
83W PRO* 3.9 29.4 - - + +
86W ALA* 5.0 0.2 - - + -
87W LEU* 4.3 13.2 - - + -
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Residues in contact with GLN 76 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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558M GLY 5.3 3.6 + - - -
560M ILE* 4.6 9.9 - - - +
78T SER* 4.6 12.4 + - - -
27W ALA* 5.0 6.5 - - - +
28W PRO* 3.9 12.4 - - - +
29W ASN 3.1 20.4 - - - +
30W ALA* 4.0 7.4 - - + +
56W VAL* 3.2 7.3 - - - +
57W LEU* 2.5 52.0 + - + +
58W PHE* 2.7 43.8 + - + +
74W ARG* 3.9 14.8 - - - +
75W ILE* 1.3 74.1 - - - +
77W THR* 1.3 59.2 + - - +
83W PRO* 5.3 0.4 - - - -
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Residues in contact with THR 77 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29W ASN* 3.0 26.2 + - - +
55W LYS 3.3 10.3 - - - +
56W VAL* 3.6 24.9 - - + -
57W LEU* 3.1 18.0 - - - +
75W ILE* 4.5 1.1 - - + -
76W GLN* 1.3 82.5 - - - +
78W THR* 1.3 64.6 + - - +
79W GLU 3.5 2.3 + - - -
81W TYR* 2.7 33.9 + - + -
83W PRO* 3.9 25.9 - - + +
86W ALA* 4.3 4.9 - - + -
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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