Contacts of the strand formed by residues 58 - 64 (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 ARG 58 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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638A LYS* 4.3 7.6 - - - +
655A ILE* 4.3 3.8 - - - -
31W GLU* 4.4 14.1 + - - +
32W MET* 5.9 0.6 - - - +
53W ILE 3.4 2.3 - - - +
54W ASN* 3.6 1.0 - - - -
55W LEU* 2.9 69.6 + - - +
56W ARG* 3.1 25.3 - - - +
57W GLY* 1.3 81.2 - - - +
59W ILE* 1.3 64.4 + - - +
60W ILE* 3.6 7.6 + - + +
83W VAL* 5.0 0.4 - - - +
85W ARG* 5.1 4.3 - - - +
90W GLU* 2.9 41.5 + - - -
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Residues in contact with ILE 59 (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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638A LYS* 4.5 20.2 - - + +
639A SER 4.6 8.3 - - - +
640A LEU* 4.2 22.2 - - + +
653A ALA* 4.0 15.0 - - + -
655A ILE* 4.3 13.2 - - + -
661A ILE* 3.5 43.7 - - + -
52W VAL* 3.7 27.4 - - + -
53W ILE 3.6 4.5 - - - +
58W ARG* 1.3 74.4 - - - +
60W ILE* 1.3 68.8 + - - +
61W PRO* 4.2 4.5 - - + +
90W GLU* 5.2 0.9 - - - +
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Residues in contact with ILE 60 (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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52W VAL* 3.3 3.7 - - - -
53W ILE* 2.9 48.7 + - + +
55W LEU* 3.6 33.9 - - + -
58W ARG* 4.0 11.9 - - + +
59W ILE* 1.3 81.2 - - - +
61W PRO* 1.4 81.9 - - + +
83W VAL* 3.9 10.1 - - + -
90W GLU* 3.2 36.1 - - + +
91W VAL* 4.1 6.3 - - - +
92W GLY* 3.7 16.6 - - - +
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Residues in contact with PRO 61 (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 5.0 8.5 - - - +
641A GLY* 5.9 3.1 - - - -
643A VAL* 3.8 29.2 - - + -
644A PHE* 3.6 26.2 - - + -
49W VAL* 5.9 0.2 - - + -
51W GLY 3.3 7.9 - - - +
52W VAL* 4.1 2.9 - - + -
59W ILE* 4.2 6.3 - - + +
60W ILE* 1.4 85.2 - - + +
62W VAL* 1.3 56.6 + - - +
63W VAL* 5.2 2.5 - - + -
90W GLU 3.5 23.8 - - - +
91W VAL* 3.8 5.0 - - + +
92W GLY 2.7 31.0 + - - -
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Residues in contact with VAL 62 (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* 3.9 21.8 - - + -
49W VAL* 3.8 0.9 - - - +
50W GLU* 2.8 27.3 + - + +
51W GLY 2.8 15.2 + - - +
53W ILE* 3.6 46.9 - - + +
60W ILE* 4.0 0.9 - - + +
61W PRO* 1.3 77.2 - - - +
63W VAL* 1.3 64.0 + - - +
81W ILE* 3.9 23.3 - - + -
92W GLY* 3.1 13.7 - - - +
94W LEU* 4.3 16.6 - - + -
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Residues in contact with VAL 63 (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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643A VAL* 5.0 6.3 - - + -
48W PHE* 3.5 8.7 - - + +
49W VAL* 3.7 24.2 - - + -
50W GLU* 4.8 1.6 - - - -
61W PRO* 5.0 0.9 - - + -
62W VAL* 1.3 81.1 - - - +
64W ASN* 1.3 58.8 + - - +
65W LEU 3.4 1.0 + - - -
68W ILE* 3.6 25.6 - - + -
91W VAL* 3.9 9.0 - - + -
92W GLY 2.7 13.5 + - - +
93W PHE* 3.6 22.7 - - + -
94W LEU* 2.9 30.0 + - - +
145W ILE* 3.7 23.1 - - + -
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Residues in contact with ASN 64 (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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48W PHE 2.8 18.8 + - - +
50W GLU* 3.3 26.5 + - - +
63W VAL* 1.3 69.2 - - - +
65W LEU* 1.3 63.5 + - - +
66W ALA* 3.2 20.4 + - - +
67W LYS* 3.0 39.0 + - + +
68W ILE* 3.2 14.0 + - - +
73W PHE* 3.5 25.0 - - - -
75W GLU* 4.9 0.4 + - - -
78W MET* 3.7 18.5 - - - +
94W LEU* 4.3 5.6 - - - -
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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