Contacts of the strand formed by residues 46 - 50 (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 ALA 46 (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* 4.2 5.1 - - - -
23A TYR* 3.2 24.9 - - + +
25A VAL* 5.7 0.2 - - + -
36A ALA* 4.1 24.0 - - + +
39A ALA* 5.0 2.5 - - + -
40A ALA* 5.0 1.3 - - + +
44A ALA 3.7 7.4 + - - +
45A ARG* 1.3 74.9 - - - +
47A ALA* 1.3 62.8 + - - +
122A HIS 4.3 5.1 + - - +
123A ILE* 3.5 20.2 - - + +
124A GLU* 3.1 22.3 + - - +
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Residues in contact with ALA 47 (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 27.1 - - + -
23A TYR 2.9 7.4 + - - +
24A LEU* 3.7 5.6 - - + -
25A VAL* 2.8 34.7 + - - +
46A ALA* 1.3 74.1 - - - +
48A VAL* 1.3 59.3 + - - +
49A VAL 4.2 0.2 - - - -
123A ILE* 4.3 0.4 - - - -
124A GLU* 3.2 11.2 - - + +
126A ILE* 3.6 27.1 - - + -
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Residues in contact with VAL 48 (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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25A VAL* 3.4 8.5 - - + +
27A GLY 4.0 5.8 - - - +
28A GLY* 3.6 34.5 - - - +
32A GLY 4.9 0.2 - - - +
33A LEU* 4.3 9.4 - - + -
36A ALA* 3.5 31.9 - - + -
47A ALA* 1.3 76.4 - - - +
49A VAL* 1.3 65.9 - - - +
50A GLU* 3.9 4.1 + - + +
54A LEU* 4.9 3.4 - - + -
118A LEU* 4.4 13.9 - - + -
123A ILE* 3.8 11.7 - - + -
124A GLU 2.9 10.8 + - - +
125A ILE* 3.5 6.0 - - + +
126A ILE* 2.8 27.1 + - - +
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Residues in contact with VAL 49 (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* 4.6 7.0 - - + -
25A VAL 2.8 21.4 + - - +
26A ILE* 4.4 7.4 - - - -
27A GLY* 2.8 32.7 + - - -
48A VAL* 1.3 73.7 - - - +
50A GLU* 1.3 62.4 + - - +
126A ILE* 3.2 27.8 - - + +
128A GLY 3.5 18.8 - - - +
130A ALA* 4.0 11.9 - - + -
140A ILE* 3.9 23.6 - - + -
142A VAL* 3.8 21.1 - - + -
479A FAD 3.7 3.9 + - + -
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Residues in contact with GLU 50 (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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28A GLY* 2.8 33.1 + - - +
48A VAL* 3.9 2.0 + - + +
49A VAL* 1.3 75.3 - - - +
51A SER* 1.3 61.4 + - - +
52A HIS* 2.8 32.2 + - - +
53A LYS 3.6 22.1 + - - -
54A LEU* 4.0 22.7 - - + +
125A ILE* 5.3 2.7 - - + -
126A ILE 2.9 8.8 + - - +
127A ARG* 3.5 17.4 - - - +
128A GLY 3.0 19.2 + - - -
479A FAD 2.8 39.1 + - - -
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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