Contacts of the helix formed by residues 52 - 59 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27I PHE* 4.1 12.8 - - + -
51I PRO* 1.4 89.2 - - + +
53I SER* 1.3 67.2 + - - +
54I PHE* 3.1 6.3 + - + -
55I LEU* 3.6 2.3 + - - +
56I ARG* 3.5 18.5 + - - +
152J VAL* 3.7 23.8 - - + -
154J GLY* 5.3 0.7 - - - -
156J GLU* 4.5 8.5 - - - +
159J ILE* 4.8 1.8 - - + -
161J ILE* 3.9 20.1 - - + +
168J ALA* 3.6 17.2 + - + +
169J VAL* 3.9 22.1 - - + +
171J ALA* 4.1 12.3 - - + -
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Residues in contact with SER 53 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16I PRO 5.7 0.3 - - - +
17I PHE* 5.6 9.6 - - - -
51I PRO 3.6 0.2 - - - -
52I PRO* 1.3 73.7 - - - +
54I PHE* 1.3 66.0 + - - +
56I ARG* 3.9 9.3 - - - -
57I ALA* 3.2 23.6 + - - +
86I PRO* 4.8 5.2 - - - +
139I SER* 4.0 19.1 + - - -
156J GLU* 2.4 31.3 + - - +
161J ILE* 3.5 18.7 - - - +
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Residues in contact with PHE 54 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16I PRO* 3.3 40.7 - - + +
17I PHE* 4.5 8.7 - - + -
23I LEU* 3.6 42.8 - - + -
24I PHE* 4.6 8.5 - + - -
27I PHE* 4.8 3.8 - + - -
48I TYR 4.0 13.2 - - - -
49I LEU* 3.4 25.6 - - + +
51I PRO* 3.3 51.6 - - + +
52I PRO* 3.1 1.7 + - + -
53I SER* 1.3 86.0 - - - +
55I LEU* 1.3 60.1 + - - +
56I ARG 3.3 0.9 - - - -
57I ALA* 3.4 8.0 - - - +
58I PRO* 3.1 21.7 - - - +
156J GLU* 6.0 0.7 - - - -
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Residues in contact with LEU 55 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49I LEU* 4.2 10.4 + - + +
51I PRO 3.7 1.6 + - - -
52I PRO 3.6 2.4 + - - +
54I PHE* 1.3 75.7 - - - +
56I ARG* 1.3 84.1 + - - +
57I ALA 3.2 0.4 - - - -
58I PRO* 3.2 22.2 - - - +
59I SER* 3.7 7.4 + - - -
47J PHE* 5.7 6.7 - - + +
68J MET* 3.6 48.9 - - + +
69J ARG 4.4 2.7 - - - +
167J PRO* 3.5 30.1 - - + +
168J ALA* 3.5 22.9 - - + +
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Residues in contact with ARG 56 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52I PRO 3.5 5.5 + - - +
53I SER* 3.9 7.4 - - - +
54I PHE 3.3 0.6 - - - -
55I LEU* 1.3 104.8 - - - +
57I ALA* 1.3 56.3 + - - +
59I SER* 3.9 5.1 + - - -
60I TRP* 2.9 25.6 + - - -
62I ASP* 2.7 51.9 + - - -
137I LEU 4.3 1.3 - - - -
138I SER* 3.6 26.3 + - - +
139I SER* 4.1 7.1 + - - +
68J MET 4.8 0.2 + - - -
161J ILE* 2.7 46.8 + - + +
162J THR* 3.7 3.4 - - - +
163J ARG 4.4 1.6 - - - -
165J GLU* 2.8 52.4 + - - +
167J PRO 4.0 1.2 + - - -
169J VAL* 4.0 5.7 - - - +
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Residues in contact with ALA 57 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12I ARG* 6.5 0.9 - - + -
16I PRO* 4.7 14.8 - - + +
53I SER 3.2 14.5 + - - +
54I PHE* 3.4 15.9 - - - +
55I LEU 3.2 0.2 - - - -
56I ARG* 1.3 73.3 - - - +
58I PRO* 1.4 65.5 - - + +
60I TRP* 3.3 37.9 + - + +
139I SER* 4.7 5.4 - - - +
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Residues in contact with PRO 58 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9I TRP* 3.9 40.4 - - + -
12I ARG* 5.4 19.3 - - + +
49I LEU* 5.7 2.5 - - + -
54I PHE 3.1 25.1 - - - +
55I LEU* 3.2 18.8 - - + +
57I ALA* 1.4 76.6 - - + +
59I SER* 1.3 60.2 + - - +
60I TRP* 3.7 3.6 + - - +
68J MET* 5.9 0.9 - - + -
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Residues in contact with SER 59 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55I LEU* 3.7 7.8 + - - -
56I ARG* 3.6 19.4 + - - -
57I ALA 3.3 0.4 - - - -
58I PRO* 1.3 82.9 - - - +
60I TRP* 1.3 54.2 + - - +
61I PHE* 2.8 7.4 + - - +
62I ASP* 2.4 56.5 + - - -
63I THR* 3.8 7.8 + - - +
163J ARG* 4.8 0.3 + - - -
165J GLU* 4.7 1.9 + - - -
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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