Contacts of the strand formed by residues 49 - 55 (chain W) in PDB entry 4JPB
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 VAL 49 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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643A VAL* 3.9 23.1 - - + +
644A PHE* 4.0 13.5 - - + -
45W SER* 3.0 36.6 + - - +
46W ARG* 3.1 18.4 + - + +
47W HIS 4.0 3.5 - - - +
48W PHE* 1.3 94.3 - - + +
50W GLU* 1.3 67.2 + - - +
51W GLY* 4.5 3.6 - - - +
61W PRO* 6.1 0.2 - - + -
62W VAL 3.8 5.2 - - - +
63W VAL* 3.7 22.4 - - + -
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Residues in contact with GLU 50 (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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39W ILE* 4.0 30.0 - - + +
41W PRO* 3.9 15.4 - - - +
42W VAL 4.5 1.3 + - - -
47W HIS 4.6 0.9 - - - +
48W PHE 3.7 2.3 + - - +
49W VAL* 1.3 83.5 - - - +
51W GLY* 1.3 58.8 + - - +
62W VAL* 2.8 17.6 + - + +
63W VAL* 5.0 2.2 - - - -
64W ASN* 3.3 31.4 + - - +
67W LYS* 3.4 20.0 + - - -
75W GLU* 4.5 8.1 - - - +
94W LEU* 3.9 14.4 - - + +
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Residues in contact with GLY 51 (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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644A PHE* 4.0 6.6 - - - -
39W ILE* 3.8 6.1 - - - +
40W THR 3.1 11.7 - - - -
42W VAL* 4.2 14.4 - - - -
49W VAL* 3.6 2.3 - - - +
50W GLU* 1.3 82.8 - - - +
52W VAL* 1.3 64.3 + - - +
61W PRO* 3.3 7.3 - - - +
62W VAL 2.8 27.8 + - - +
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Residues in contact with VAL 52 (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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640A LEU* 4.6 5.8 - - + +
644A PHE* 3.7 25.4 - - + -
661A ILE* 4.4 20.2 - - + -
663A LEU* 4.5 6.1 - - + -
39W ILE* 4.3 0.2 - - - -
40W THR* 2.8 53.7 + - + +
42W VAL* 4.1 11.4 - - + -
51W GLY* 1.3 78.2 - - - +
53W ILE* 1.3 65.3 - - - +
59W ILE* 3.7 28.3 - - + -
60W ILE 3.3 7.6 - - - +
61W PRO* 4.1 1.6 - - + -
62W VAL 4.5 0.2 - - - +
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Residues in contact with ILE 53 (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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661A ILE* 4.6 5.8 - - - -
34W ILE* 3.8 28.9 - - + -
38W ASP 3.3 25.4 - - - +
39W ILE* 4.0 10.8 - - + -
52W VAL* 1.3 77.7 - - - +
54W ASN* 1.3 60.8 + - - +
55W LEU* 4.2 16.6 - - + -
58W ARG 3.4 2.9 - - - +
59W ILE* 3.6 4.9 - - - +
60W ILE* 2.9 52.9 + - + +
62W VAL* 3.6 25.1 - - + -
81W ILE* 4.5 8.1 - - + -
83W VAL* 5.2 2.2 - - + -
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Residues in contact with ASN 54 (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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655A ILE* 3.2 26.7 - - - +
659A GLY* 2.8 34.7 + - - +
661A ILE* 3.7 17.2 - - + +
38W ASP 5.6 0.2 + - - -
53W ILE* 1.3 74.1 - - - +
55W LEU* 1.3 63.0 + - - +
56W ARG 4.3 0.7 + - - -
57W GLY* 3.2 27.5 + - - +
58W ARG 3.6 3.1 - - - -
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Residues in contact with LEU 55 (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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32W MET* 3.6 34.3 - - + -
34W ILE* 3.7 29.6 - - + -
53W ILE* 3.8 15.4 + - + -
54W ASN* 1.3 75.7 + - - +
56W ARG* 1.3 75.6 + - + +
57W GLY 3.1 0.2 - - - -
58W ARG* 2.9 57.6 + - - +
60W ILE* 3.6 18.4 - - + -
83W VAL* 4.9 4.7 - - + -
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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