Contacts of the strand formed by residues 30 - 34 (chain I) 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 GLN 30 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27I GLN* 3.0 19.1 + - - +
28I PRO 3.2 3.1 - - - +
29I TRP* 1.3 82.0 - - - +
31I ALA* 1.3 60.7 + - - +
43I SER* 3.6 18.9 + - - -
44I GLY 3.9 2.0 - - - -
66I GLY 4.1 3.6 - - - +
67I LEU* 3.9 13.6 - - - +
69I GLY 4.4 4.0 + - - -
70I LEU 5.3 3.4 + - - +
139I SER* 2.8 40.7 + - - +
140I GLY* 3.7 0.2 - - - -
141I TRP* 3.7 26.1 - - + -
155I LEU* 3.5 24.1 - - + +
198I PRO* 3.0 27.4 - - - +
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Residues in contact with ALA 31 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29I TRP 4.3 1.6 - - - +
30I GLN* 1.3 73.2 - - - +
32I ALA* 1.3 60.8 + - - +
33I LEU* 4.5 0.9 - - + -
43I SER* 3.0 9.5 + - - -
44I GLY* 2.7 50.2 + - - +
45I VAL* 4.8 0.2 - - - -
46I LEU 4.9 0.2 - - - +
52I VAL* 4.2 11.7 - - + -
65I ILE* 3.9 21.5 - - + -
66I GLY 3.7 4.9 - - - -
67I LEU* 4.0 9.0 - - + -
141I TRP* 4.4 3.0 - - - -
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Residues in contact with ALA 32 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30I GLN 4.3 0.2 - - - -
31I ALA* 1.3 71.2 - - - +
33I LEU* 1.3 65.2 + - - +
34I VAL* 4.0 4.9 - - + +
40I LEU* 3.7 13.7 - - + -
42I CYS 4.1 0.9 - - - -
64I THR 3.7 0.9 - - - +
65I ILE* 3.2 8.5 - - - -
66I GLY 2.9 38.3 + - - +
70I LEU* 4.2 12.8 - - + -
73I LEU* 4.8 4.7 - - + -
141I TRP* 3.5 29.1 - - + -
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Residues in contact with LEU 33 (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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31I ALA* 4.0 7.9 - - + +
32I ALA* 1.3 82.8 - - - +
34I VAL* 1.3 62.4 + - - +
40I LEU* 3.1 4.2 - - - +
41I PHE* 2.9 51.9 + - + -
42I CYS* 3.0 24.5 + - + +
43I SER 3.9 27.6 - - - +
44I GLY* 4.1 3.4 - - - +
52I VAL* 5.0 3.1 - - + -
54I SER* 4.3 7.4 - - - +
58I CYS* 4.6 5.4 - - + +
63I TYR* 4.4 9.6 - - + -
64I THR 4.2 2.9 - - - +
65I ILE* 4.2 20.0 - - + -
106I ILE* 4.2 19.7 - - + -
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Residues in contact with VAL 34 (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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32I ALA* 5.1 5.8 - - + +
33I LEU* 1.3 75.4 - - - +
35I MET* 1.3 65.7 + - - +
37I ASN 5.1 1.6 - - - -
38I GLU* 3.0 17.9 - - - +
40I LEU* 3.7 19.3 - - + +
41I PHE* 3.7 7.1 - - - -
63I TYR* 5.2 0.9 - - - -
64I THR* 3.2 51.8 + - + +
66I GLY 5.7 0.7 - - - +
73I LEU* 5.5 7.4 - - + -
82I MET* 4.9 15.7 - - + -
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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