Contacts of the strand formed by residues 58 - 65 (chain B) in PDB entry 2JJ6
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 GLN 58 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B ALA* 3.2 0.2 - - - -
53B VAL* 2.6 52.1 + - + +
56B ASP* 3.3 30.4 + - + +
57B ARG* 1.3 75.1 + - - +
59B LEU* 1.3 59.6 + - - +
60B LEU* 3.6 27.3 - - + +
72B GLU* 5.6 0.2 - - - +
74B SER* 4.8 13.0 + - - -
76B ILE* 6.3 0.2 - - - -
79B PHE* 3.1 8.9 - - - -
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Residues in contact with LEU 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B LEU* 4.6 11.2 - - + -
51B LYS 3.1 20.6 - - - +
52B ALA* 3.8 10.5 - - + -
58B GLN* 1.3 72.9 - - - +
60B LEU* 1.3 61.3 + - - +
61B ARG* 3.1 26.4 + - + +
74B SER* 3.8 9.0 + - - +
76B ILE* 3.4 40.5 - - + +
79B PHE* 4.5 7.6 - - + -
80B PRO* 4.9 2.7 - - + -
81B PHE* 3.7 28.7 - - + -
107B LEU* 3.8 11.7 - - + -
108B PHE* 3.7 22.7 - - + -
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Residues in contact with LEU 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B GLU* 3.3 2.1 - - - +
50B LEU* 3.6 1.7 - - - -
51B LYS* 2.7 55.0 + - + +
53B VAL* 4.3 17.9 - - + -
58B GLN* 3.6 31.4 - - + +
59B LEU* 1.3 74.5 - - - +
61B ARG* 1.3 61.5 + - - +
72B GLU* 3.8 35.2 - - + +
73B GLN 3.5 4.3 - - - +
74B SER* 3.7 22.0 - - - -
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Residues in contact with ARG 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B ILE* 4.9 0.4 - - + -
49B GLU* 2.9 10.3 - - - +
50B LEU* 3.9 8.3 - - + -
59B LEU* 3.1 15.6 + - + +
60B LEU* 1.3 78.3 - - - +
62B ASN* 1.3 65.6 + - - +
71B GLU 3.8 1.4 - - - +
72B GLU* 3.4 2.6 - - - +
73B GLN* 3.0 55.7 + - + +
74B SER* 2.9 24.3 + - - -
75B ALA* 2.4 36.0 + - - +
76B ILE* 3.4 12.1 - - - +
108B PHE* 3.4 55.8 - - + +
109B ASP 5.0 1.0 + - - -
110B PHE* 3.8 20.4 - - + -
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Residues in contact with ASN 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B ILE* 3.5 3.6 - - - -
49B GLU* 2.8 35.4 + - - +
60B LEU* 6.4 0.2 - - + -
61B ARG* 1.3 76.8 - - - +
63B SER* 1.3 76.9 + - - +
69B ARG* 3.9 33.5 - - - +
70B GLY 2.9 39.7 + - - +
71B GLU 3.8 2.9 - - - -
72B GLU* 3.3 22.5 - - + +
110B PHE* 3.7 6.6 - - - -
113B ARG* 2.9 14.9 + - - +
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Residues in contact with SER 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B VAL* 3.2 17.5 - - - -
47B ALA* 3.5 14.4 - - - -
62B ASN* 1.3 88.2 + - - +
64B CYS* 1.3 64.0 + - - +
65B ILE* 5.0 7.5 - - - +
68B GLU 4.2 0.8 + - - -
69B ARG* 3.4 8.5 - - - -
70B GLY* 3.3 15.4 + - - -
110B PHE* 4.2 0.2 - - - -
113B ARG* 3.0 40.8 + - - +
114B ILE* 5.6 0.2 - - - -
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Residues in contact with CYS 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B PRO* 6.4 2.5 - - - -
45B ASP* 3.2 9.2 - - - +
46B VAL* 2.8 48.2 + - + +
63B SER* 1.3 78.2 - - - +
65B ILE* 1.3 61.6 + - - +
67B GLY* 3.7 34.8 - - - -
68B GLU 3.0 5.2 - - - -
69B ARG* 4.1 22.0 - - - +
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Residues in contact with ILE 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B ASP* 3.3 14.4 - - - +
46B VAL 4.8 0.2 - - - +
63B SER* 5.0 4.0 - - - +
64B CYS* 1.3 80.1 - - - +
66B SER* 1.3 76.5 + - - +
67B GLY 3.1 0.4 - - - -
68B GLU* 2.8 37.8 + - + +
113B ARG* 4.2 25.8 - - + +
114B ILE* 3.5 34.1 - - + -
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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