Contacts of the helix formed by residues 51 - 63 (chain A) in PDB entry 2JRF
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 THR 51 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45A ALA* 4.6 1.3 - - - -
47A GLY* 3.2 33.4 - - - +
49A SER 4.0 3.3 + - - +
50A VAL* 1.3 74.5 - - - +
52A GLY* 1.3 66.7 + - - +
53A THR* 4.0 6.7 + - - -
54A ASP* 3.1 22.4 + - - +
55A VAL* 3.0 25.2 + - - +
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Residues in contact with GLY 52 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45A ALA* 4.8 5.1 - - - +
51A THR* 1.3 72.1 - - - +
53A THR* 1.3 62.5 + - - +
55A VAL* 3.0 20.1 + - - +
56A ASP* 2.8 21.4 + - - +
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Residues in contact with THR 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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51A THR* 3.4 6.6 + - - -
52A GLY* 1.3 72.2 - - - +
54A ASP* 1.3 58.5 + - - +
56A ASP* 2.9 26.1 + - + +
57A ILE* 2.9 34.1 + - + +
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Residues in contact with ASP 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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49A SER 5.0 4.0 - - - +
50A VAL* 4.2 11.7 - - + +
51A THR* 3.1 27.4 + - - +
53A THR* 1.3 77.3 - - - +
55A VAL* 1.3 57.5 + - - +
57A ILE* 3.2 16.1 + - - +
58A VAL* 3.0 36.4 + - - +
85A LYS* 2.8 43.5 + - - +
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Residues in contact with VAL 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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35A TRP* 3.0 46.3 + - + +
36A ALA* 4.3 13.9 - - + -
39A CYS* 3.4 24.5 - - + -
45A ALA* 3.7 18.8 - - + -
50A VAL* 3.5 21.5 - - + -
51A THR 3.0 20.6 + - - +
52A GLY* 3.2 9.6 - - - +
54A ASP* 1.3 77.6 - - - +
56A ASP* 1.3 62.0 + - - +
58A VAL* 3.6 6.8 + - - +
59A PHE 3.3 9.7 + - - -
82A LEU* 4.8 0.9 - - + -
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Residues in contact with ASP 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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32A GLY* 4.6 14.2 - - - +
35A TRP* 5.2 1.8 - - - +
36A ALA* 4.8 10.9 - - - +
52A GLY 2.8 23.8 + - - +
53A THR* 2.9 11.9 + - + +
55A VAL* 1.3 74.7 - - - +
57A ILE* 1.3 62.0 + - + +
59A PHE* 3.4 8.0 + - - +
60A SER* 2.8 30.5 + - - -
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Residues in contact with ILE 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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53A THR* 2.9 35.0 + - + +
54A ASP* 3.3 17.5 - - - +
56A ASP* 1.3 75.3 - - + +
58A VAL* 1.3 54.6 + - + +
60A SER* 3.0 8.6 + - - -
61A LYS* 2.8 61.2 + - + +
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Residues in contact with VAL 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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35A TRP* 4.6 1.8 - - + -
54A ASP* 3.0 28.7 + - - +
55A VAL* 3.8 6.3 - - - +
56A ASP 3.4 0.2 - - - -
57A ILE* 1.3 73.9 - - + +
59A PHE* 1.3 63.7 + - - +
61A LYS* 3.1 13.2 + - - +
62A VAL* 3.0 31.8 + - + +
78A ALA* 3.7 28.7 - - + -
81A GLU* 3.6 37.9 - - + +
82A LEU* 3.8 18.6 - - + -
85A LYS* 4.7 1.3 - - - -
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Residues in contact with PHE 59 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A MET 3.2 24.7 - - - -
31A ASN 3.8 7.4 - - - -
32A GLY* 3.2 30.3 - - - -
35A TRP* 3.6 36.5 - + + +
55A VAL 3.3 4.1 + - - +
56A ASP* 3.6 10.5 - - - +
57A ILE 3.2 0.4 - - - -
58A VAL* 1.3 80.2 - - - +
60A SER* 1.3 61.8 + - - +
61A LYS 3.4 0.3 + - - -
62A VAL* 3.7 7.4 - - - +
63A LYS* 3.3 54.9 + - - +
68A ARG 3.5 11.9 - - - -
69A VAL* 3.8 5.8 - - - -
70A ILE* 3.5 30.4 - - + +
78A ALA* 5.8 0.2 - - - -
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Residues in contact with SER 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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56A ASP 2.8 18.1 + - - -
57A ILE* 3.0 8.7 + - - -
59A PHE* 1.3 76.7 - - - +
61A LYS* 1.3 60.1 + - - +
63A LYS* 3.4 29.2 + - - +
64A GLY 4.8 0.3 + - - -
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Residues in contact with LYS 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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57A ILE* 2.8 33.3 + - + +
58A VAL* 3.1 24.8 + - - +
60A SER* 1.3 77.8 - - - +
62A VAL* 1.3 69.6 + - + +
63A LYS 3.2 2.5 + - - -
64A GLY* 3.6 11.3 + - - -
81A GLU* 2.6 32.6 + - - -
85A LYS* 5.0 5.9 - - - +
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Residues in contact with VAL 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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58A VAL* 3.0 27.1 + - + +
59A PHE* 3.7 11.4 - - - +
61A LYS* 1.3 76.9 - - + +
63A LYS* 1.3 66.9 + - - +
64A GLY* 3.4 0.9 + - - -
70A ILE* 3.9 18.4 - - + -
74A GLU* 3.0 40.2 - - + +
77A LYS* 4.3 14.8 - - + -
78A ALA* 4.1 25.6 - - + +
81A GLU* 5.7 2.0 - - + +
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Residues in contact with LYS 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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59A PHE* 3.3 46.6 - - - +
60A SER* 3.4 26.2 + - - +
62A VAL* 1.3 80.6 - - - +
64A GLY* 1.3 66.5 + - - +
65A LYS* 2.8 27.3 + - - +
66A SER* 3.0 23.8 + - - +
67A ALA* 2.7 30.0 + - + -
68A ARG* 4.4 3.8 + - - +
70A ILE* 3.6 18.4 - - + -
74A GLU* 3.2 13.5 - - - +
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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