Contacts of the strand formed by residues 55 - 62 (chain B) in PDB entry 3DAE
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 55 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B ALA 3.8 0.2 - - - +
51B HIS* 5.2 0.2 - - - -
52B ILE* 2.9 45.3 + - + +
53B GLY 3.4 22.9 - - - -
54B ASN* 1.3 79.3 - - + +
56B GLN* 1.3 63.4 + - - +
57B ILE* 3.4 4.2 + - - +
72B ALA* 4.3 9.9 - - + -
73B TYR* 3.4 4.3 - - - +
74B HIS* 3.9 39.2 + + + -
81B VAL* 4.0 24.7 - - + -
83B LEU* 5.1 9.0 - - + -
119B TYR* 3.7 14.5 - + - +
120B ASP* 4.3 12.8 - - + +
122B ILE* 5.6 5.6 - - + -
131B VAL* 3.5 39.2 - - + +
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Residues in contact with GLN 56 (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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50B ALA* 4.5 5.4 - - - -
51B HIS* 5.6 9.0 - - + +
52B ILE 5.2 0.2 - - - +
54B ASN 4.0 0.4 + - - -
55B TYR* 1.3 70.3 - - - +
57B ILE* 1.3 65.7 + - - +
58B VAL* 3.5 6.2 + - + +
72B ALA* 3.2 17.8 - - - -
73B TYR* 3.0 54.0 + - + -
75B THR* 3.7 33.3 + - - +
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Residues in contact with ILE 57 (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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50B ALA* 3.3 44.5 + - - +
52B ILE* 3.8 23.3 - - + -
55B TYR 3.4 1.7 + - - +
56B GLN* 1.3 72.9 - - - +
58B VAL* 1.3 65.5 + - - +
59B LYS* 4.2 8.5 - - - +
70B LYS* 3.9 39.5 - - + +
71B LEU 3.6 11.7 - - - +
72B ALA* 3.6 1.6 - - - -
83B LEU* 4.2 16.4 - - + -
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Residues in contact with VAL 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B GLN* 3.7 13.2 - - + +
57B ILE* 1.3 76.6 - - - +
59B LYS* 1.3 76.7 + - + +
71B LEU* 2.8 34.6 + - + +
72B ALA* 4.2 7.0 - - - -
73B TYR* 4.3 17.0 - - + -
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Residues in contact with LYS 59 (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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57B ILE* 4.2 4.0 - - - +
58B VAL* 1.3 94.3 - - + +
60B THR* 1.3 72.5 + - + +
61B LEU* 3.4 30.6 + - + +
70B LYS* 3.6 4.5 - - - +
71B LEU* 2.8 36.8 + - + +
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Residues in contact with THR 60 (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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59B LYS* 1.3 78.0 + - + +
61B LEU* 1.3 61.7 - - - +
62B GLY 3.3 19.2 + - - -
63B GLU* 5.7 0.3 - - - +
68B LYS* 4.1 17.8 - - + +
69B VAL 3.8 6.2 + - - -
70B LYS* 4.1 18.8 - - - +
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Residues in contact with LEU 61 (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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59B LYS* 3.4 28.4 + - - +
60B THR* 1.3 74.4 - - - +
62B GLY* 1.3 59.2 + - - +
69B VAL* 2.9 17.5 + - + +
70B LYS 4.1 4.9 - - - +
71B LEU* 3.4 46.4 - - + +
82B ALA* 5.2 3.8 - - + -
134B TYR* 4.1 33.2 - - + +
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Residues in contact with GLY 62 (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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60B THR* 3.3 13.1 + - - -
61B LEU* 1.3 81.3 - - - +
63B GLU* 1.3 67.0 + - - +
68B LYS* 3.8 1.0 - - - -
69B VAL* 3.1 27.2 + - - +
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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