Contacts of the strand formed by residues 57 - 67 (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 ARG 57 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53O ASN* 3.6 8.4 - - - -
54O THR* 2.9 47.1 + - - +
55O GLN 4.1 9.2 - - - -
56O GLY* 1.3 82.7 - - - +
58O ASP* 1.3 64.2 + - - +
60O GLU* 3.7 9.8 + - - +
77O ARG* 3.2 34.9 - - - +
123O TYR* 2.6 34.2 + - - -
124O PHE 5.1 0.4 + - - -
126O GLU* 3.7 25.6 - - - +
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Residues in contact with ASP 58 (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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53O ASN* 3.0 12.5 + - - +
56O GLY 4.1 1.4 - - - -
57O ARG* 1.3 71.5 - - - +
59O ASN* 1.3 76.0 + - - +
60O GLU 3.2 0.2 - - - -
77O ARG* 2.8 40.2 + - + +
137O GLN 2.7 12.3 - - - +
138O ASP* 3.3 20.9 - - - +
329O CA 2.4 30.9 - - - -
350Q CPJ 3.1 7.4 - - - +
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Residues in contact with ASN 59 (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 4.5 0.2 - - - -
53O ASN* 3.2 10.4 + - - -
58O ASP* 1.3 78.8 + - - +
60O GLU* 1.3 63.8 + - - +
61O LEU* 3.4 2.5 - - - -
62O LEU* 3.6 18.6 - - + +
74O TYR* 3.8 32.3 - - + +
76O GLY 3.5 1.0 + - - -
77O ARG* 2.8 25.8 + - + +
136O GLU* 3.0 6.9 - - - +
329O CA 2.3 27.0 - - - -
350Q CPJ 2.9 35.7 + - - +
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Residues in contact with GLU 60 (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* 3.3 27.7 + - + +
54O THR* 4.1 13.5 - - + +
57O ARG* 3.7 22.0 + - - +
58O ASP 3.1 1.8 + - - -
59O ASN* 1.3 76.5 - - - +
61O LEU* 1.3 59.8 + - - +
75O ILE* 3.4 9.2 - - - +
76O GLY* 2.8 21.1 + - - +
77O ARG* 3.0 24.9 + - - -
123O TYR* 2.5 35.1 + - - -
125O VAL* 3.3 5.4 - - + +
126O GLU* 3.0 31.6 + - - +
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Residues in contact with LEU 61 (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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30O LEU* 4.7 0.4 - - + -
33O PHE* 3.6 44.9 - - + -
35O LEU* 5.1 1.3 - - + -
50O PHE* 3.7 17.6 - - + +
52O TYR* 2.9 65.1 + - + +
60O GLU* 1.3 78.1 - - - +
62O LEU* 1.3 65.6 + - - +
63O VAL* 4.7 3.1 - - + -
73O LEU* 3.8 13.5 - - + -
74O TYR 3.2 5.4 - - - +
75O ILE* 4.7 2.2 - - + -
125O VAL* 4.6 9.9 - - + -
159O MET* 3.7 27.6 - - + -
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Residues in contact with LEU 62 (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* 3.3 27.4 - - - +
50O PHE 3.3 10.1 - - - +
51O SER* 4.0 6.7 - - - -
52O TYR 5.2 0.7 - - - +
59O ASN* 3.6 17.3 - - - -
61O LEU* 1.3 77.6 - - - +
63O VAL* 1.3 67.2 + - - +
64O TYR* 4.1 7.0 - - + -
72O SER 3.6 1.2 - - - +
73O LEU* 3.3 6.4 - - - +
74O TYR* 2.7 65.8 + - + -
136O GLU* 3.5 29.4 - - + +
350Q CPJ 3.5 21.5 - - + -
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Residues in contact with VAL 63 (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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35O LEU* 3.8 19.3 - - + -
37O PHE* 4.2 11.0 - - + -
49O LEU* 2.9 44.5 + - + -
50O PHE* 3.0 21.9 + - + +
61O LEU* 4.7 3.1 - - + -
62O LEU* 1.3 78.4 - - - +
64O TYR* 1.3 62.7 + - - +
71O TYR* 5.3 3.4 - - + -
72O SER 3.5 8.1 - - - +
73O LEU* 4.2 9.2 - - + -
94O ILE* 4.9 2.5 - - + -
96O VAL* 3.8 26.2 - - + -
107O PHE* 4.1 17.3 - - + -
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Residues in contact with TYR 64 (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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46O ALA* 3.4 29.5 - - + +
47O TYR 3.4 22.9 - - - -
48O SER* 3.8 13.2 - - - -
49O LEU* 5.1 0.2 - - - -
62O LEU* 4.1 6.7 - - + -
63O VAL* 1.3 77.3 - - - +
65O LYS* 1.3 59.8 + - - +
66O GLU* 3.5 33.8 + - + -
71O TYR* 3.8 1.8 - - - -
72O SER* 2.8 39.2 + - - +
74O TYR* 3.9 24.9 - + + -
136O GLU* 4.5 0.9 - - + -
148O GLN* 3.1 42.6 + - + +
350Q CPJ 4.0 25.0 - - + -
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Residues in contact with LYS 65 (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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43O LEU 5.3 2.0 + - - -
45O ARG 4.5 1.2 - - - +
46O ALA* 3.2 2.1 - - - +
47O TYR* 2.9 79.6 + - + +
49O LEU* 4.2 11.0 - - + +
64O TYR* 1.3 71.1 - - - +
66O GLU* 1.3 63.7 - - - +
67O ARG 3.7 15.5 - - - +
68O VAL* 4.0 15.4 - - - +
69O GLY 4.3 0.9 - - - +
70O GLU 3.4 14.8 - - - +
71O TYR* 3.4 31.4 + - + +
86O GLU* 3.0 28.9 + - - -
88O PHE* 5.1 7.3 - - - -
92O VAL* 6.2 0.9 - - + +
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Residues in contact with GLU 66 (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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44O SER 4.9 0.2 - - - +
45O ARG 4.4 0.3 - - - -
46O ALA* 3.3 27.9 + - - +
64O TYR* 3.5 25.0 - - + +
65O LYS* 1.3 72.9 - - - +
67O ARG* 1.3 86.9 + - - +
70O GLU* 3.6 17.9 + - + +
72O SER* 3.0 31.4 + - - +
74O TYR* 3.7 3.1 + - - -
79O LYS* 3.4 24.5 + - - -
81O THR* 4.8 4.3 - - + -
350Q CPJ 6.0 0.3 - - - +
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Residues in contact with ARG 67 (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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44O SER 4.4 12.3 - - - +
45O ARG 5.4 1.3 - - - -
65O LYS* 3.5 11.9 - - - +
66O GLU* 1.3 94.6 + - - +
68O VAL* 1.3 75.5 + - - +
69O GLY 3.2 0.5 + - - -
70O GLU* 2.8 71.5 + - - +
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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