Contacts of the strand formed by residues 82 - 90 (chain A) in PDB entry 2JGB
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 82 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63A TRP* 3.8 26.9 - - + -
64A TYR 3.5 10.1 - - - +
65A SER* 4.1 3.6 - - - -
67A ARG* 5.0 0.4 - - - +
78A TYR* 3.5 27.0 + - + +
79A GLU* 3.3 30.4 - - + +
80A GLN 4.2 3.7 - - - +
81A ASN* 1.3 79.3 - - - +
83A LYS* 1.3 64.6 + - - +
114A HIS* 3.4 29.2 - - + +
122A PRO* 3.1 37.9 - - + -
123A MET* 5.1 4.0 - - + -
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Residues in contact with LYS 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A TRP* 3.1 9.6 - - - -
64A TYR* 2.9 72.1 + - + +
81A ASN 5.6 0.7 - - - +
82A ILE* 1.3 77.3 - - - +
84A GLN* 1.3 67.7 + - - +
85A ILE* 3.6 8.0 + - + +
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Residues in contact with GLN 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A THR* 3.7 21.0 + - + +
62A PHE 3.6 4.7 - - - -
63A TRP* 3.5 42.0 - - + -
83A LYS* 1.3 80.1 - - - +
85A ILE* 1.3 61.6 + - - +
86A GLY* 4.8 2.0 - - - +
87A THR* 4.2 7.3 + - - -
121A LYS* 6.2 0.6 - - - +
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Residues in contact with ILE 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A PHE* 2.8 24.1 + - + +
63A TRP 4.3 6.3 - - - +
64A TYR* 3.8 31.4 - - + +
83A LYS* 4.3 8.3 - - - +
84A GLN* 1.3 75.0 - - - +
86A GLY* 1.3 60.9 + - - +
97A PHE* 4.1 19.4 - - + -
101A MET* 3.7 35.2 - - + -
113A PHE* 4.3 3.8 - - + -
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Residues in contact with GLY 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A TYR 4.1 0.3 - - - +
61A THR* 3.4 4.2 - - - +
62A PHE* 2.9 30.1 + - - +
84A GLN* 3.7 1.8 - - - +
85A ILE* 1.3 83.8 - - - +
87A THR* 1.3 62.4 + - - -
88A PHE* 4.7 0.3 - - - -
97A PHE* 3.6 22.9 - - - -
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Residues in contact with THR 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A VAL* 3.9 32.8 - - + +
59A ASN* 4.6 0.7 - - + -
60A TYR 3.3 12.3 - - - +
61A THR* 2.9 21.7 + - - +
84A GLN* 4.2 6.9 + - - -
86A GLY* 1.3 75.6 - - - -
88A PHE* 1.3 67.5 + - - +
93A GLN* 4.8 0.2 - - - +
97A PHE* 3.5 13.2 - - - -
118A GLU* 3.6 34.8 + - + +
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Residues in contact with PHE 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A VAL* 4.0 3.6 - - - -
56A LEU* 3.6 29.2 - - + -
59A ASN* 3.3 7.1 - - - +
60A TYR* 2.9 58.7 + - + -
62A PHE* 3.7 18.2 - + - -
86A GLY 4.7 0.7 - - - -
87A THR* 1.3 77.4 - - - +
89A ALA* 1.3 60.7 - - - +
90A SER 3.8 1.6 - - - -
93A GLN* 3.5 27.4 - - + +
94A PHE* 3.7 35.2 - + + +
97A PHE* 4.1 16.4 - + + -
115A LEU* 3.7 24.7 - - + -
156A LEU* 3.9 12.3 - - + -
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Residues in contact with ALA 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A VAL* 3.7 13.9 - - + +
48A VAL* 3.6 25.8 - - - -
49A PRO* 3.7 12.3 - - + +
56A LEU* 3.2 28.4 + - - +
59A ASN* 3.2 24.3 - - - +
88A PHE* 1.3 72.6 - - - +
90A SER* 1.3 61.3 + - - +
93A GLN* 2.7 13.8 + - - +
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Residues in contact with SER 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A PRO* 3.9 9.4 - - - -
53A GLU* 2.6 41.5 + - - -
54A HIS 3.2 13.9 - - - -
56A LEU* 3.7 10.6 - - - +
88A PHE* 3.8 0.9 - - - -
89A ALA* 1.3 80.8 - - - +
91A VAL* 1.3 65.2 + - - +
92A GLU 3.5 1.7 + - - -
93A GLN* 2.9 19.4 + - - +
94A PHE* 2.9 22.5 + - - +
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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