Contacts of the strand formed by residues 47 - 54 (chain O) in PDB entry 2A3W
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 47 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39O ALA* 6.2 0.2 - - - +
41O SER* 4.0 18.7 + - - -
43O LEU* 3.8 36.3 + - + -
44O SER 5.5 0.2 - - - -
45O ARG* 3.2 25.1 - - - +
46O ALA* 1.3 75.5 - - - +
48O SER* 1.3 62.1 + - - +
49O LEU* 3.5 26.0 - - + -
64O TYR* 3.4 10.5 - - - -
65O LYS* 2.9 76.3 + - + +
148O GLN 3.5 6.3 - - - +
149O SER 3.6 23.3 - - - +
150O PHE* 3.6 21.7 - + - -
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Residues in contact with SER 48 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47O TYR* 1.3 75.8 - - - +
49O LEU* 1.3 62.6 + - - +
50O PHE 3.6 6.6 + - - -
51O SER* 3.7 11.4 - - - -
62O LEU* 3.3 21.1 - - - +
63O VAL 3.9 1.3 - - - -
64O TYR* 3.8 7.5 - - - -
132O VAL 5.2 0.2 + - - -
134O GLY 4.9 4.2 + - - -
135O GLN 4.1 3.0 + - - -
136O GLU* 3.6 36.1 - - - -
148O GLN 3.1 9.3 + - - -
150O PHE* 3.5 25.1 + - - +
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Residues in contact with LEU 49 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37O PHE* 3.5 29.3 - - + -
39O ALA* 4.3 12.3 - - + -
47O TYR* 3.5 26.3 + - + -
48O SER* 1.3 74.6 - - - +
50O PHE* 1.3 62.8 + - - +
63O VAL* 2.9 22.4 + - + +
65O LYS* 4.2 26.5 - - + +
71O TYR* 4.3 5.2 - - + -
94O ILE* 3.9 22.0 - - + -
132O VAL 5.2 0.7 - - - -
133O LEU* 3.9 19.4 - - - +
134O GLY 5.1 0.4 + - - -
150O PHE* 3.7 20.9 - - + -
154O ILE* 4.0 16.1 - - + +
157O LEU* 5.9 0.5 - - - +
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Residues in contact with PHE 50 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22O LEU* 4.2 5.4 - - + -
35O LEU* 3.5 37.2 - - + -
37O PHE* 4.5 4.3 - - + -
48O SER* 3.6 2.4 + - - -
49O LEU* 1.3 81.4 - - - +
51O SER* 1.3 59.2 + - - +
52O TYR* 3.9 21.8 - + + -
61O LEU* 4.2 20.4 - - + -
62O LEU* 3.3 7.8 - - - +
63O VAL* 3.0 33.2 + - + -
131O ILE* 3.5 31.2 - - + -
132O VAL 4.3 2.2 - - - -
133O LEU* 3.9 15.7 - - + -
157O LEU* 4.0 8.7 - - + -
159O MET* 3.9 14.4 - - - -
183O LEU* 3.8 23.1 - - + -
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Residues in contact with SER 51 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48O SER* 3.7 9.4 - - - -
50O PHE* 1.3 73.5 - - - +
52O TYR* 1.3 61.1 + - - +
53O ASN* 4.1 3.1 + - - -
62O LEU* 4.0 8.7 - - - +
131O ILE* 3.3 3.8 - - - +
132O VAL 2.9 36.9 + - - -
135O GLN 3.6 23.1 - - - -
136O GLU* 4.2 2.1 + - - -
137O GLN* 2.9 43.3 + - - +
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Residues in contact with TYR 52 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26O LEU* 3.6 20.8 - - + +
30O LEU* 4.0 2.9 - - + +
50O PHE* 3.9 13.5 - + + -
51O SER* 1.3 73.2 + - - +
53O ASN* 1.3 65.1 + - - +
54O THR* 3.9 7.0 - - + -
59O ASN* 4.2 0.3 - - - -
60O GLU* 3.3 10.4 + - + -
61O LEU* 2.9 69.3 + - + +
62O LEU* 4.9 0.8 - - - +
125O VAL* 3.5 21.5 + - + +
126O GLU 2.6 30.2 + - - -
129O PRO* 3.4 28.6 - - + +
130O LYS 3.5 4.0 - - - -
131O ILE* 3.7 22.7 - - + -
159O MET* 4.5 10.3 - - + -
182O ILE* 6.1 0.2 - - + -
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Residues in contact with ASN 53 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51O SER* 4.1 3.6 + - - -
52O TYR* 1.3 77.3 + - - +
54O THR* 1.3 67.5 + - - +
57O ARG 3.6 10.6 + - - +
58O ASP* 3.0 30.5 + - - +
59O ASN* 3.2 18.0 + - - +
60O GLU* 4.4 0.4 - - - -
62O LEU* 6.0 0.2 - - - +
129O PRO* 3.3 5.1 - - - +
130O LYS 2.8 32.1 + - - -
136O GLU* 4.9 0.5 - - - +
137O GLN* 3.5 34.3 + - - +
138O ASP 4.0 1.2 - - - -
139O SER 3.4 23.5 + - - +
140O TYR* 3.6 4.7 - - - -
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Residues in contact with THR 54 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52O TYR* 3.9 11.4 - - + -
53O ASN* 1.3 80.4 + - - +
55O GLN* 1.3 66.6 + - - +
56O GLY 3.2 0.9 + - - -
57O ARG* 2.9 49.5 + - - +
60O GLU* 4.1 4.6 - - + +
126O GLU* 3.4 29.0 + - + +
127O ALA 3.4 25.8 - - - +
128O GLN 4.4 2.0 - - - -
129O PRO* 4.1 3.4 - - + -
140O TYR* 3.4 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