Contacts of the strand formed by residues 63 - 67 (chain L) in PDB entry 2BDI
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 63 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33L LEU* 4.4 13.2 - - + -
34L VAL 5.2 1.8 - - - -
41L PHE* 4.6 4.7 - + + -
58L CYS 3.7 7.4 - - - -
59L PHE* 3.4 1.6 - - - -
60L GLN* 3.1 52.4 + - + -
62L SER* 1.3 75.3 - - - +
64L THR* 1.3 64.5 + - - +
65L ILE* 3.8 18.4 - - + -
84L GLU* 3.8 6.2 - - - +
85L ALA 2.9 37.1 + - - +
86L SER 4.7 4.5 - - - -
88L SER* 2.9 40.7 + - - -
104L MET* 3.2 13.7 - - + -
106L ILE* 3.5 43.7 - - + -
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Residues in contact with THR 64 (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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32L ALA 3.7 0.5 - - - +
33L LEU* 4.9 0.4 - - - -
34L VAL* 3.2 55.4 + - + +
35L MET* 5.1 2.6 + - - -
62L SER 5.3 0.2 + - - -
63L TYR* 1.3 75.1 + - - +
65L ILE* 1.3 61.9 + - - +
82L MET* 5.2 15.2 - - + +
83L VAL 3.8 10.8 - - - +
84L GLU* 4.7 11.0 - - + +
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Residues in contact with ILE 65 (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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31L ALA* 3.9 23.6 - - + -
32L ALA 3.2 9.0 - - - +
33L LEU* 4.2 11.7 - - + -
52L VAL* 4.1 14.6 - - + -
63L TYR* 3.8 13.2 + - + -
64L THR* 1.3 72.3 - - - +
66L GLY* 1.3 60.6 + - - +
67L LEU* 4.2 14.8 - - + -
81L GLN 3.6 0.9 - - - +
82L MET* 3.4 3.8 - - - -
83L VAL* 3.0 42.6 + - + +
85L ALA* 4.4 7.6 - - + +
106L ILE* 3.9 28.7 - - + -
108L LEU* 3.5 24.5 - - + -
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Residues in contact with GLY 66 (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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30L GLN 4.1 1.4 - - - +
31L ALA* 3.7 3.5 - - - -
32L ALA* 2.9 33.6 + - - +
34L VAL* 5.8 0.4 - - - +
64L THR 3.8 1.4 + - - -
65L ILE* 1.3 72.7 - - - +
67L LEU* 1.3 63.6 + - - -
70L LEU* 3.6 17.8 - - - +
81L GLN 3.7 0.4 - - - -
82L MET* 3.5 25.3 - - - -
141L TRP* 5.6 0.3 - - - -
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Residues in contact with LEU 67 (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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28L PRO 5.3 1.6 - - - +
29L TRP 5.0 0.2 - - - +
30L GLN 4.0 16.2 - - - +
31L ALA* 4.0 15.9 - - + -
46L LEU* 4.3 28.9 - - + -
52L VAL* 5.1 0.7 - - + -
65L ILE* 4.2 9.2 - - + -
66L GLY* 1.3 76.4 - - - +
69L GLY* 1.3 65.1 + - - +
70L LEU* 3.1 6.0 + - - +
80L SER* 3.3 4.0 - - - -
81L GLN 3.0 30.0 + - - +
83L VAL* 4.6 13.9 - - + -
108L LEU* 5.1 3.4 - - + -
112L VAL* 3.8 37.2 - - + -
118L ILE* 3.3 21.1 - - + -
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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