Contacts of the strand formed by residues 30 - 34 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27F GLN* 2.9 20.5 + - + +
28F PRO 3.2 3.1 - - - +
29F TRP* 1.3 81.5 - - - +
31F ALA* 1.3 60.5 - - - +
43F SER* 3.5 19.2 + - - -
44F GLY 3.9 2.0 - - - -
66F GLY 4.1 4.2 - - - +
67F LEU* 3.9 14.0 - - - +
69F GLY 4.4 3.5 + - - -
70F LEU 5.3 4.0 + - - +
139F SER* 2.8 40.4 + - - +
140F GLY* 3.7 0.2 - - - -
141F TRP* 3.6 27.4 - - + -
155F LEU* 3.5 22.4 - - + +
198F PRO* 3.1 26.3 - - - +
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Residues in contact with ALA 31 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29F TRP 4.3 1.8 - - - +
30F GLN* 1.3 74.0 - - - +
32F ALA* 1.3 60.6 + - - +
33F LEU* 4.5 1.1 - - + -
43F SER* 2.9 9.9 - - - -
44F GLY* 2.7 51.4 + - - +
45F VAL* 4.3 0.4 - - - +
46F LEU 4.9 0.4 - - - +
52F VAL* 4.2 12.1 - - + -
65F ILE* 4.0 20.2 - - + -
66F GLY 3.7 4.0 - - - -
67F LEU* 4.0 9.4 - - + -
141F TRP* 4.5 2.9 - - - -
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Residues in contact with ALA 32 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30F GLN 4.3 0.2 - - - -
31F ALA* 1.3 70.5 - - - +
33F LEU* 1.3 64.2 + - - +
34F VAL* 4.0 5.3 - - + +
40F LEU* 3.7 15.3 - - + -
42F CYS 4.2 0.9 - - - -
64F THR 3.8 0.7 - - - +
65F ILE* 3.2 7.6 - - - -
66F GLY 2.9 38.5 + - - +
70F LEU* 4.2 13.5 - - + -
73F LEU* 4.8 5.2 - - + -
141F TRP* 3.6 28.4 - - + -
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Residues in contact with LEU 33 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31F ALA* 3.9 8.1 - - + +
32F ALA* 1.3 80.4 - - - +
34F VAL* 1.3 60.9 + - - +
40F LEU* 3.2 4.4 - - - +
41F PHE* 3.0 49.5 + - + -
42F CYS* 3.3 30.3 + - + +
43F SER 3.9 22.4 - - - +
44F GLY* 4.1 3.6 - - - +
52F VAL* 5.0 3.6 - - + -
54F SER* 4.3 7.2 - - - +
58F CYS* 4.7 4.5 - - + +
63F TYR* 4.4 9.6 - - + -
64F THR 4.2 3.6 - - - +
65F ILE* 4.2 20.4 - - + -
104F MET* 5.2 0.2 - - + -
106F ILE* 4.2 20.0 - - + -
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Residues in contact with VAL 34 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32F ALA* 5.1 5.4 - - + +
33F LEU* 1.3 76.9 - - - +
35F MET* 1.3 65.8 + - - +
37F ASN* 5.1 1.6 - - - -
38F GLU* 3.0 19.1 - - - +
40F LEU* 3.7 19.5 - - + +
41F PHE* 3.7 6.8 - - - -
63F TYR* 5.2 1.0 - - - -
64F THR* 3.2 50.0 + - + +
66F GLY 5.7 0.4 - - - +
73F LEU* 5.5 6.7 - - + -
82F MET* 4.8 16.8 - - + -
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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