Contacts of the helix formed by residues 52 - 59 (chain L) in PDB entry 2YGD
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 PRO 52 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50L ARG* 3.2 16.6 - - - +
51L PRO* 1.4 81.4 - - + +
53L SER* 1.3 62.2 + - - +
54L PHE 3.3 0.4 - - - -
55L LEU* 3.1 25.2 + - + +
56L ARG* 3.5 18.4 + - - +
67L GLU* 3.6 16.8 - - - +
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Residues in contact with SER 53 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27L PHE* 4.3 15.3 - - - -
51L PRO* 3.0 2.4 + - - -
52L PRO* 1.3 76.1 - - - +
54L PHE* 1.3 56.7 + - - +
56L ARG* 3.1 8.4 + - - +
57L ALA* 2.8 32.0 + - - +
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Residues in contact with PHE 54 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13L PRO* 3.6 48.5 - - + -
14L PHE* 3.4 34.1 - + - -
23L LEU* 3.3 31.6 - - + -
27L PHE* 3.6 28.1 - + + -
49L LEU* 3.4 33.2 - - + +
51L PRO 3.4 5.8 + - - +
52L PRO 3.2 0.6 + - - -
53L SER* 1.3 76.8 - - - +
55L LEU* 1.3 63.1 + - + +
56L ARG 3.1 0.2 - - - -
57L ALA* 3.9 5.7 - - + +
58L PRO* 3.0 27.0 - - - +
70L LEU* 3.8 15.0 - - + -
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Residues in contact with LEU 55 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47L PHE* 6.5 0.2 - - + -
49L LEU* 3.5 33.4 - - + +
50L ARG* 3.5 22.4 - - - +
51L PRO 3.8 0.9 - - - +
52L PRO* 3.1 24.3 + - + +
54L PHE* 1.3 87.9 - - + +
56L ARG* 1.3 77.5 + - - +
58L PRO* 4.2 1.6 - - - -
67L GLU* 3.9 6.1 - - - +
68L MET* 3.9 21.1 - - + -
69L ARG* 3.5 25.6 - - + +
70L LEU* 3.5 11.7 + - + +
71L GLU* 3.3 23.4 - - - +
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Residues in contact with ARG 56 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52L PRO* 3.5 16.2 + - - +
53L SER* 3.1 11.8 + - - +
55L LEU* 1.3 112.4 + - - +
57L ALA* 1.3 64.0 + - - +
58L PRO* 3.4 2.2 - - - -
59L SER 3.2 3.8 + - - -
60L TRP* 3.1 41.1 + - + +
63L THR 4.4 4.7 - - - -
64L GLY* 3.4 34.0 + - - +
66L SER 3.9 8.0 + - - -
67L GLU* 2.7 31.5 + - - +
69L ARG* 3.7 9.7 - - - +
71L GLU* 3.6 14.1 + - - -
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Residues in contact with ALA 57 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13L PRO* 5.1 9.0 - - + +
16L PRO* 6.0 4.9 - - + -
53L SER 2.8 21.3 + - - +
54L PHE* 3.9 6.5 - - + +
56L ARG* 1.3 71.3 - - - +
58L PRO* 1.4 65.6 - - + +
60L TRP* 3.4 25.9 - - - -
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Residues in contact with PRO 58 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9L TRP* 4.1 11.7 - - + +
12L ARG* 3.1 31.4 + - + +
13L PRO* 4.0 32.8 - - + -
54L PHE 3.0 26.9 - - - +
56L ARG 3.5 4.3 - - - +
57L ALA* 1.4 82.2 - - + +
59L SER* 1.3 62.1 + - - +
60L TRP* 5.0 2.4 - - - -
70L LEU* 3.0 35.7 - - + +
71L GLU* 4.3 1.3 - - + -
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Residues in contact with SER 59 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9L TRP* 4.2 10.6 - - - -
56L ARG* 3.2 5.9 + - - +
57L ALA 3.3 0.8 + - - -
58L PRO* 1.3 84.6 - - - +
60L TRP* 1.3 61.9 + - - +
61L PHE* 3.0 16.8 - - - +
62L ASP* 2.4 53.9 + - - +
63L THR 4.1 0.7 + - - -
64L GLY 5.3 0.2 + - - -
71L GLU* 3.6 20.5 - - - +
72L LYS 4.6 0.9 + - - -
74L ARG* 4.4 3.3 + - - -
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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