Contacts of the strand formed by residues 58 - 65 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A LYS 3.5 1.4 - - - +
52A ALA* 3.5 0.3 - - - -
53A VAL* 2.8 33.4 + - + +
56A ASP* 4.1 27.4 + - + +
57A ARG* 1.3 81.9 + - - +
59A LEU* 1.3 61.4 + - - +
60A LEU* 3.9 20.4 - - + -
74A SER* 3.4 37.8 + - - +
76A ILE* 4.6 6.7 - - - +
79A PHE* 3.3 6.5 - - - -
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Residues in contact with LEU 59 (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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30A PHE* 5.8 0.9 - - + -
50A LEU* 4.5 11.4 - - + -
51A LYS 3.4 26.0 - - - +
52A ALA* 3.8 9.2 - - + +
58A GLN* 1.3 76.6 + - - +
60A LEU* 1.3 60.2 + - - +
61A ARG* 3.0 25.0 + - - -
74A SER* 3.7 6.1 - - - +
76A ILE* 4.2 18.4 - - + +
79A PHE* 4.6 5.2 - - + -
80A PRO* 4.2 4.0 - - + -
81A PHE* 3.9 28.3 - - + -
100A VAL* 6.3 0.2 - - + -
102A VAL* 5.0 2.5 - - + -
107A LEU* 4.1 18.6 - - + -
108A PHE* 3.6 32.1 - - + -
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Residues in contact with LEU 60 (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 GLU* 3.3 3.4 - - - +
50A LEU* 3.6 1.7 - - - -
51A LYS* 2.8 53.9 + - + +
53A VAL* 4.3 20.0 - - + -
56A ASP* 5.9 1.3 - - - +
58A GLN* 4.0 22.4 - - + -
59A LEU* 1.3 73.3 - - - +
61A ARG* 1.3 62.6 + - - +
72A GLU* 3.7 38.4 - - + +
73A GLN 3.4 2.0 - - - -
74A SER* 3.5 27.4 - - - -
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Residues in contact with ARG 61 (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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48A ILE* 5.0 0.2 - - + -
49A GLU* 3.1 5.8 - - - +
50A LEU* 3.7 17.0 - - + -
59A LEU* 3.0 24.3 + - - -
60A LEU* 1.3 77.2 - - - +
62A ASN* 1.3 65.8 + - - +
71A GLU 3.8 1.4 - - - +
72A GLU* 3.4 3.9 - - - +
73A GLN* 2.8 52.9 + - + +
74A SER 3.2 12.1 + - - +
75A ALA* 3.0 39.1 + - - +
76A ILE* 3.3 9.9 - - - +
108A PHE* 3.5 54.5 - - + +
109A ASP 4.9 4.6 + - - -
110A PHE* 3.8 21.7 - - + -
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Residues in contact with ASN 62 (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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48A ILE* 3.4 4.5 - - - -
49A GLU* 2.8 36.9 + - - +
61A ARG* 1.3 74.5 - - - +
63A SER* 1.3 73.8 + - - +
69A ARG* 3.7 36.6 - - - +
70A GLY 2.9 34.6 + - - +
71A GLU 3.7 5.6 - - - -
72A GLU* 3.6 20.4 + - + +
110A PHE* 3.7 7.7 - - - -
113A ARG* 2.8 23.2 + - - +
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Residues in contact with SER 63 (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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46A VAL* 3.3 18.2 - - - -
47A ALA* 3.5 13.9 - - - -
62A ASN* 1.3 82.5 + - - +
64A CYS* 1.3 63.2 + - - +
65A ILE* 4.3 8.0 - - - +
68A GLU 5.3 0.2 + - - -
69A ARG* 3.3 9.5 - - - +
70A GLY* 3.0 26.6 + - - -
113A ARG* 3.0 38.7 + - - +
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Residues in contact with CYS 64 (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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43A PRO* 6.3 3.8 - - - -
44A ALA 5.5 2.2 - - - +
45A ASP* 3.2 10.1 - - - +
46A VAL* 2.8 50.9 + - + +
63A SER* 1.3 76.0 - - - +
65A ILE* 1.3 61.0 + - - +
66A SER 4.2 0.2 - - - -
67A GLY* 3.6 37.0 - - - -
68A GLU 3.3 6.1 - - - -
69A ARG* 4.4 19.5 - - - +
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Residues in contact with ILE 65 (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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45A ASP* 3.6 13.0 - - - +
46A VAL 4.8 0.2 - - - +
63A SER* 4.8 4.7 - - - +
64A CYS* 1.3 81.7 - - - +
66A SER* 1.3 82.2 + - - +
68A GLU* 2.9 31.5 + - + +
113A ARG* 4.3 25.1 - - + +
114A ILE* 3.8 31.2 - - + -
115B GLN* 6.5 0.9 - - - -
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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