Contacts of the helix formed by residues 47 - 51 (chain B) in PDB entry 3OUY
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 SER 47 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46B GLY* 1.3 71.1 - - - -
48B TYR* 1.3 65.6 + - - +
50B ARG* 3.4 1.7 + - - +
51B ASN* 3.2 4.2 + - - -
52B THR* 2.8 47.1 + - - -
53B TRP* 3.3 26.4 + - - +
59B GLU* 4.6 4.5 + - - +
152B LYS* 3.8 0.9 - - - -
176B GLU* 5.1 0.2 - - - -
702B POP 2.8 51.2 + - - -
35D A 3.9 0.4 + - - -
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Residues in contact with TYR 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B GLY* 3.5 15.8 - - - -
25B ARG* 2.6 33.0 + - - -
28B GLU* 2.9 41.0 + - + +
44B PHE* 4.7 5.4 - + + -
45B VAL 4.5 5.4 - - - +
46B GLY 3.0 1.0 + - - -
47B SER* 1.3 83.7 + - - +
49B ALA* 1.3 65.6 + - + +
50B ARG 3.1 5.5 + - - -
51B ASN* 3.3 9.0 + - - -
53B TRP* 3.7 25.1 - + - -
58B LEU* 3.6 27.4 - - + -
59B GLU 3.1 18.1 + - - +
60B ILE* 3.7 40.2 - - + -
61B ASP* 4.7 1.5 + - - +
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Residues in contact with ALA 49 (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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44B PHE* 3.6 24.9 - - + +
45B VAL 3.4 19.9 + - - +
46B GLY 2.9 3.4 + - - -
48B TYR* 1.3 80.4 - - + +
50B ARG* 1.3 64.3 + - - +
51B ASN 3.7 0.2 - - - -
134B HIS* 3.4 24.2 + - + +
138B GLU* 5.9 0.3 - - - +
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Residues in contact with ARG 50 (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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45B VAL* 4.7 0.2 - - - +
46B GLY 3.3 27.9 + - - +
47B SER 4.0 0.4 - - - +
48B TYR 3.1 0.8 - - - -
49B ALA* 1.3 75.1 - - - +
51B ASN* 1.3 73.0 + - - +
52B THR* 3.3 14.0 + - - +
133B HIS 4.7 0.4 - - - -
134B HIS* 2.9 58.6 + - + +
137B LEU* 3.7 32.4 - - - +
138B GLU* 4.2 11.7 - - - +
141B ILE* 4.3 20.6 - - + +
142B LYS* 6.2 3.6 - - - +
145B GLU* 4.3 3.5 - - - +
173B TYR* 5.0 0.4 - - - -
176B GLU* 2.8 42.4 + - - +
35D A 3.4 29.5 + - - -
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Residues in contact with ASN 51 (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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21B VAL* 6.2 0.2 - - - +
25B ARG* 3.5 24.3 + - - +
47B SER 3.2 3.8 + - - -
48B TYR 3.3 6.1 + - - -
49B ALA 3.7 0.4 - - - -
50B ARG* 1.3 79.7 - - - +
52B THR* 1.3 56.3 + - - +
53B TRP* 3.8 15.6 - - - -
145B GLU* 3.1 28.9 - - + +
149B ARG* 3.2 31.5 + - - -
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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