Contacts of the strand formed by residues 49 - 58 (chain A) in PDB entry 2JDC
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 LYS 49 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A LEU* 6.2 0.4 - - - -
18A ARG* 4.8 9.4 - - - +
45A TYR* 3.2 9.1 - - - -
46A TYR 2.9 34.3 + - - +
47A GLY 4.7 2.2 - - - +
48A GLY* 1.3 80.3 - - - +
50A LEU* 1.3 71.7 + - - +
51A ILE* 3.4 15.1 + - + +
78A LEU* 3.5 27.8 - - - -
81A TYR* 3.9 17.3 - - - +
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Residues in contact with LEU 50 (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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7A ILE* 4.5 6.5 - - + -
11A ASP* 3.5 28.3 - - + +
15A LEU* 3.7 23.0 - - + +
43A GLY* 3.6 18.4 - - - -
44A GLY 3.7 5.4 - - - +
45A TYR* 3.6 35.6 - - + +
49A LYS* 1.3 81.7 - - - +
51A ILE* 1.3 63.3 + - - +
52A SER 3.4 22.7 - - - +
53A ILE* 4.1 12.8 - - + -
78A LEU* 4.9 0.2 - - - +
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Residues in contact with ILE 51 (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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2A ILE* 4.0 14.1 - - + -
15A LEU* 4.0 8.2 - - - +
44A GLY 2.8 19.1 + - - +
46A TYR* 3.7 19.7 - - + +
49A LYS* 3.8 20.4 - - + +
50A LEU* 1.3 80.4 - - - +
52A SER* 1.3 59.8 + - - +
77A THR* 3.3 5.5 - - - +
78A LEU* 2.8 33.1 + - + -
81A TYR* 3.6 53.4 - - + -
86A ALA* 3.7 27.8 - - + -
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Residues in contact with SER 52 (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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15A LEU* 4.1 1.0 - - - +
43A GLY* 3.2 5.4 - - - -
44A GLY* 2.8 28.8 + - - -
50A LEU* 3.4 2.8 - - - +
51A ILE* 1.3 81.4 - - - +
53A ILE* 1.3 68.1 + - - +
75A MET* 3.8 7.4 - - - +
76A ALA 3.2 7.5 + - - -
77A THR* 2.9 21.8 + - - -
86A ALA* 3.8 19.1 - - - -
87A GLY 3.8 5.0 + - - -
90A LEU* 3.5 17.4 - - - +
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Residues in contact with ILE 53 (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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7A ILE* 3.9 22.2 - - + -
12A THR* 3.6 35.9 - - + +
15A LEU* 3.7 22.2 - - + -
16A ARG* 3.6 25.8 - - + +
42A LEU 3.5 4.9 - - - +
50A LEU* 4.1 9.9 - - + -
52A SER* 1.3 80.0 - - - +
54A ALA* 1.3 65.0 + - - +
74A GLY 3.1 16.2 - - - +
75A MET* 3.3 5.2 - - - +
76A ALA* 2.9 45.0 + - + +
90A LEU* 3.6 3.1 - - - -
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Residues in contact with ALA 54 (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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12A THR* 5.6 0.4 - - - +
41A HIS* 3.4 3.3 - - - +
42A LEU* 2.9 32.4 + - + +
53A ILE* 1.3 78.7 - - - +
55A SER* 1.3 62.6 + - - +
56A PHE* 3.7 26.7 - - + -
72A LEU* 3.8 10.5 - - + -
73A ARG 4.2 1.1 - - - -
74A GLY 3.8 6.5 - - - -
75A MET* 4.1 10.5 - - - -
90A LEU* 4.0 16.8 - - + -
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Residues in contact with SER 55 (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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12A THR* 4.0 5.9 - - - +
16A ARG* 2.9 23.4 + - - -
34A ASP* 4.5 2.0 - - - -
40A PHE 3.5 4.7 - - - -
41A HIS* 2.7 30.2 + - - -
53A ILE* 5.9 0.2 - - - +
54A ALA* 1.3 74.9 - - - +
56A PHE* 1.3 63.7 + - - +
57A HIS* 5.7 0.7 - - - -
71A GLN 3.7 0.2 - - - +
72A LEU* 3.3 6.6 - - - +
73A ARG* 2.8 47.7 + - - +
74A GLY 5.0 1.0 + - - -
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Residues in contact with PHE 56 (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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39A ALA* 3.1 5.5 - - - +
40A PHE* 2.9 73.2 + + + +
41A HIS* 5.3 0.4 - - - -
42A LEU* 4.3 7.2 - - + -
54A ALA* 3.7 36.8 - - + -
55A SER* 1.3 78.0 - - - +
57A HIS* 1.3 63.2 + - - +
70A TYR* 4.2 6.5 - - + -
71A GLN 3.3 5.6 - - - +
72A LEU* 3.7 17.3 - - + -
90A LEU 4.5 1.6 - - - -
91A ILE* 4.0 13.7 - - + -
94A ALA* 3.2 30.7 - - + -
98A LEU* 4.5 4.0 - - + -
106A LEU* 3.9 30.7 - - + -
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Residues in contact with HIS 57 (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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33A SER* 3.3 35.2 + - - +
36A LEU* 3.6 28.8 - - + +
37A ARG 4.7 0.7 - - - +
39A ALA* 4.0 22.2 - - + +
55A SER 5.5 0.4 + - - -
56A PHE* 1.3 79.0 + - - +
58A GLN* 1.3 82.6 + - - +
59A ALA* 3.8 8.4 - - + +
70A TYR* 3.2 11.3 - - - -
71A GLN* 2.9 71.1 + - + -
73A ARG* 4.6 5.1 - - + +
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Residues in contact with GLN 58 (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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36A LEU* 5.2 3.1 - - - +
37A ARG 4.3 15.5 + - - +
57A HIS* 1.3 81.3 - - - +
59A ALA* 1.3 59.9 + - - +
60A GLU* 3.0 25.2 + - - +
67A GLN 5.2 0.6 + - - -
68A LYS* 3.2 40.7 + - + +
69A GLN 3.2 17.7 - - - +
70A TYR* 3.4 21.3 + - + +
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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