Contacts of the helix formed by residues 52 - 63 (chain J) in PDB entry 5G04
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 52 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23J LEU* 4.0 12.8 - - - +
47J LEU* 2.9 42.7 + - + +
50J THR* 4.3 14.6 - - + +
51J ALA* 1.3 77.3 - - - +
53J TYR* 1.3 64.3 + - - +
54J HIS 3.4 2.0 - - - -
55J ARG* 3.3 27.4 + - + +
56J ALA* 3.1 17.7 + - - +
263K PHE 4.1 5.5 + - - -
265K ALA* 4.4 13.6 - - - +
295K TYR* 3.0 44.7 + - + +
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Residues in contact with TYR 53 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48J TYR* 3.2 49.7 + + - -
51J ALA* 3.3 31.5 + - + +
52J GLN* 1.3 72.5 - - - +
54J HIS* 1.3 67.8 + - - +
56J ALA* 3.1 1.5 + - - -
57J ALA* 2.9 10.2 + - - +
79J CYS* 2.6 39.5 - - - +
82J ALA* 3.6 41.9 - - + +
83J ALA* 4.3 11.7 - - + -
295K TYR* 4.3 1.2 + - - -
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Residues in contact with HIS 54 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52J GLN 3.4 0.4 - - - -
53J TYR* 1.3 78.7 - - - +
55J ARG* 1.3 55.8 + - - +
57J ALA* 3.5 8.1 + - + +
58J HIS* 3.0 34.7 + - + +
80J HIS* 5.4 10.3 + - - -
83J ALA* 5.5 2.1 - - - +
85J GLU* 6.1 5.0 - - - +
262K PRO* 3.9 14.8 - - + +
263K PHE* 3.6 28.5 - + + -
290K LYS* 6.3 0.4 - - - +
294K LEU* 3.4 39.0 - - + +
295K TYR* 4.7 4.6 + - - +
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Residues in contact with ARG 55 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23J LEU* 4.0 15.6 - - - +
27J ASP* 4.3 12.7 + - - -
43J LEU* 5.3 0.2 - - - +
47J LEU* 3.4 36.7 - - + +
52J GLN* 3.3 25.7 + - - +
53J TYR 3.2 0.2 - - - -
54J HIS* 1.3 73.7 - - - +
56J ALA* 1.3 60.8 + - - +
58J HIS* 3.3 1.7 + - - +
59J ALA* 3.0 29.1 + - - +
261K ASP* 3.1 32.6 + - - +
262K PRO* 4.4 7.1 - - + +
263K PHE* 3.1 23.5 + - + +
264K HIS* 3.0 17.5 + - - +
265K ALA* 2.9 35.0 - - - +
295K TYR* 3.6 15.7 + - - +
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Residues in contact with ALA 56 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44J ALA* 3.5 26.1 - - + +
47J LEU* 3.5 19.2 - - + +
48J TYR* 3.8 9.0 - - + +
52J GLN 3.1 7.5 + - - +
53J TYR 3.1 2.5 + - - +
55J ARG* 1.3 73.5 - - - +
57J ALA* 1.3 67.0 + - - +
59J ALA* 3.2 4.8 + - - +
60J LEU* 3.2 29.3 + - + +
75J LEU* 5.9 1.3 - - + -
79J CYS* 3.5 19.7 - - + -
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Residues in contact with ALA 57 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53J TYR 2.9 15.7 + - - +
54J HIS* 3.7 9.9 - - + +
56J ALA* 1.3 79.1 - - - +
58J HIS* 1.3 56.5 - - - +
60J LEU* 3.3 3.9 + - - +
61J ARG* 2.9 35.0 + - - +
76J ALA* 4.9 5.4 - - - +
79J CYS* 3.5 13.8 - - + -
80J HIS* 3.6 34.3 - - + +
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Residues in contact with HIS 58 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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520F ARG* 5.6 8.1 - - - -
54J HIS* 3.0 24.1 + - + +
55J ARG 3.7 2.5 - - - +
56J ALA 3.2 0.2 - - - -
57J ALA* 1.3 76.1 - - - +
59J ALA* 1.3 57.5 + - - +
61J ARG* 5.0 2.0 - - - -
62J SER* 3.0 62.7 + - - +
63J ARG* 6.1 0.2 - - - -
259K GLU 3.6 17.9 + - - -
260K LYS 3.4 15.4 + - - -
262K PRO* 3.3 43.2 - - + +
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Residues in contact with ALA 59 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40J ILE* 4.2 12.8 - - + +
43J LEU* 5.1 8.5 - - + -
44J ALA* 4.8 7.6 - - + -
47J LEU* 4.7 9.4 - - + -
55J ARG 3.0 16.8 + - - +
56J ALA* 3.6 7.9 - - - +
58J HIS* 1.3 76.8 - - - +
60J LEU* 1.3 63.2 + - - +
63J ARG* 3.6 46.9 + - - +
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Residues in contact with LEU 60 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40J ILE* 4.3 6.7 - - + +
41J TYR* 4.9 1.6 - - - -
44J ALA* 3.5 33.7 - - + -
56J ALA* 3.2 12.3 + - + +
57J ALA 3.9 2.7 - - - +
59J ALA* 1.3 79.8 - - - +
61J ARG* 1.3 62.2 + - - +
64J LYS 3.8 1.0 + - - -
65J LEU* 3.5 42.4 + - + +
66J ASP* 3.8 10.1 + - + -
72J CYS* 3.7 33.0 - - + +
75J LEU* 3.8 12.6 - - + -
76J ALA* 3.7 37.2 - - + +
79J CYS* 6.2 0.4 - - + -
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Residues in contact with ARG 61 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57J ALA* 2.9 17.3 + - - +
58J HIS* 4.5 2.5 - - - +
60J LEU* 1.3 77.4 - - - +
62J SER* 1.3 65.7 + - - +
64J LYS* 3.2 17.8 + - - +
66J ASP* 3.7 22.1 + - - +
76J ALA* 4.6 9.6 - - + -
80J HIS* 3.7 26.8 - - - -
88J GLN* 4.7 17.2 + - - +
91J ASP* 5.8 1.0 - - - +
92J VAL* 3.3 34.8 - - - +
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Residues in contact with SER 62 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58J HIS* 3.0 49.7 + - - -
59J ALA 4.7 1.3 - - - -
61J ARG* 1.3 79.0 - - - +
63J ARG* 1.3 70.2 + - - +
64J LYS* 3.2 11.3 + - - +
260K LYS 5.3 2.5 - - - -
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Residues in contact with ARG 63 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35J GLU* 2.7 46.6 + - + +
40J ILE* 3.8 27.8 - - + +
43J LEU* 5.8 6.7 - - - +
58J HIS* 4.9 1.0 + - - -
59J ALA* 3.6 42.2 + - - +
60J LEU 4.0 0.2 + - - -
61J ARG 3.4 0.4 - - - -
62J SER* 1.3 80.4 - - - +
64J LYS* 1.3 63.7 + - - +
65J LEU* 2.9 22.4 + - + +
68J LEU* 5.4 2.8 - - - +
231K LEU* 5.5 12.5 - - - +
260K LYS* 5.0 19.9 + - - +
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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