Contacts of the helix formed by residues 103 - 107 (chain B) in PDB entry 1YDY
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 TYR 103 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80B HIS* 3.6 37.8 - + - +
81B TYR* 4.5 7.4 - + + -
82B LEU* 4.4 0.2 - - - -
95B ARG 5.3 0.6 + - - -
97B ARG* 3.4 32.5 - - + +
99B ASP* 2.5 40.6 + - - -
101B ARG* 3.6 23.2 + - + -
102B TYR* 1.3 72.3 - - - +
104B ALA* 1.3 66.5 + - - +
105B ILE* 4.2 12.8 - - + +
106B ASP* 3.0 26.2 + - - +
107B PHE* 3.1 17.9 - - - -
177B PHE* 3.7 24.0 - + - -
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Residues in contact with ALA 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B VAL* 3.9 27.1 - - + -
68B MET 3.8 5.2 - - - +
69B THR* 3.7 6.7 - - + -
75B VAL* 5.1 4.0 - - + -
77B LEU* 3.9 15.3 - - + -
80B HIS* 3.0 18.0 + - + +
81B TYR* 4.2 0.8 - - - +
82B LEU* 4.0 16.8 - - + +
102B TYR 3.9 2.2 + - - -
103B TYR* 1.3 71.2 - - - +
105B ILE* 1.3 62.6 + - - +
107B PHE* 3.1 22.7 + - - +
112B ILE* 4.5 5.8 - - + +
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Residues in contact with ILE 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B MET 3.4 16.5 + - - +
69B THR 4.2 0.9 - - - +
70B LYS* 3.0 27.8 - - - +
80B HIS 4.6 0.8 + - - -
97B ARG* 3.5 27.1 - - - +
103B TYR* 3.1 6.5 - - + +
104B ALA* 1.3 77.0 - - - +
106B ASP* 1.3 60.2 + - - +
107B PHE 3.4 0.4 - - - -
177B PHE* 3.9 21.1 - - + -
178B HIS* 4.2 18.4 - - + +
181B GLU* 3.5 31.0 - - + +
183B LYS* 3.5 38.3 - - + -
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Residues in contact with ASP 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B LYS* 3.4 17.0 + - - +
95B ARG* 2.9 30.8 + - - +
97B ARG* 2.8 54.2 + - - +
103B TYR* 3.0 18.8 + - - +
105B ILE* 1.3 79.5 - - - +
107B PHE* 1.3 67.9 + - + +
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Residues in contact with PHE 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B THR* 3.4 3.1 - - - +
70B LYS* 2.8 24.9 + - - -
82B LEU* 3.7 17.9 - - + -
88B VAL* 3.9 15.5 - - + -
92B PHE* 3.7 32.3 - + + -
95B ARG* 3.5 44.0 - - + -
102B TYR* 4.2 13.2 - + + -
103B TYR 3.1 29.2 - - - -
104B ALA 3.1 7.1 + - - +
106B ASP* 1.3 88.3 - - + +
108B THR* 1.3 63.4 + - - +
111B GLU* 3.4 17.9 - - + +
112B ILE* 3.4 24.7 - - + -
115B LEU* 6.1 0.7 - - + -
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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