Contacts of the strand formed by residues 23 - 26 (chain A) in PDB entry 1BWC
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 23 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A TYR* 3.3 4.8 - - - +
22A ASP* 1.3 81.0 - - + +
24A LEU* 1.3 60.3 + - - +
25A VAL* 3.8 18.2 - - + -
35A SER* 3.1 38.4 + - - -
36A ALA* 4.5 3.8 - - - -
39A ALA* 3.5 21.5 - - + -
44A ALA* 4.7 2.2 - - + -
45A ARG 3.2 3.6 + - - +
46A ALA* 3.2 13.0 - - + +
47A ALA 2.9 27.0 + - - +
149A ALA* 4.1 1.1 - - - -
151A HIS* 3.3 26.5 - - + -
152A ILE 4.8 0.4 - - - -
153A LEU* 3.5 32.8 - - + +
327A TYR* 4.9 1.3 - + - -
349A LEU* 3.6 14.6 - - - +
350A ALA* 5.0 1.8 + - + -
353A LEU* 4.0 16.8 - - + -
354A PHE* 3.7 17.0 - + + -
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Residues in contact with LEU 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A TYR* 3.9 26.0 - - + -
23A TYR* 1.3 74.1 - - - +
25A VAL* 1.3 63.2 + - - +
26A ILE* 4.1 1.6 - - + -
47A ALA* 3.7 13.0 - - + +
49A VAL* 4.6 6.3 - - + -
126A ILE* 4.2 9.0 - - + -
140A ILE* 3.4 37.9 - - + -
147A TYR* 4.2 23.8 - - + +
148A THR* 4.5 3.4 - - - +
149A ALA* 3.7 12.5 - - + +
151A HIS 3.0 6.5 + - - +
152A ILE* 3.3 28.2 - - + +
153A LEU 2.9 25.1 + - - -
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Residues in contact with VAL 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A TYR* 3.8 34.3 - - + -
24A LEU* 1.3 77.6 - - - +
26A ILE* 1.3 65.8 + - - +
27A GLY 3.5 21.3 + - - +
32A GLY* 3.6 22.2 - - - +
36A ALA* 4.2 16.4 - - + +
46A ALA* 5.7 0.4 - - + -
47A ALA 2.8 17.9 + - - +
48A VAL* 3.4 8.2 - - + -
49A VAL* 2.8 30.1 + - - +
153A LEU* 3.6 15.5 - - + +
155A ALA* 4.7 0.2 - - + -
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Residues in contact with ILE 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A LEU* 5.3 2.0 - - + -
25A VAL* 1.3 71.9 - - - +
27A GLY* 1.3 62.2 + - - +
49A VAL* 4.2 8.5 - - + -
130A ALA* 3.7 27.6 - - + -
132A PHE* 4.0 22.0 - - + -
140A ILE* 3.8 29.2 - - + -
152A ILE* 4.1 11.0 - - + -
153A LEU 2.8 17.4 + - - +
154A ILE* 4.5 7.6 - - + -
155A ALA* 2.8 34.3 + - - +
156A THR* 3.6 21.4 + - + -
298A LEU* 4.4 7.0 - - + -
479A FAD 3.9 12.1 - - + +
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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