Contacts of the strand formed by residues 57 - 67 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53A ASN* 3.6 8.2 - - - -
54A THR* 2.9 42.0 + - - +
55A GLN 3.5 19.5 + - - -
56A GLY* 1.3 90.8 + - - +
58A ASP* 1.3 63.0 + - - +
60A GLU* 3.6 8.6 - - - +
77A ARG* 3.5 34.4 - - - +
123A TYR* 5.3 0.9 - - - -
126A GLU* 3.9 26.5 + - - -
139A SER 6.4 0.2 - - - -
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Residues in contact with ASP 58 (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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53A ASN* 2.9 14.2 + - - +
56A GLY 4.2 1.0 + - - -
57A ARG* 1.3 72.5 - - - +
59A ASN* 1.3 70.2 + - - +
60A GLU 3.2 0.2 - - - -
77A ARG* 2.8 41.8 + - + +
137A GLN 2.8 12.1 - - - +
138A ASP* 3.3 20.1 - - - +
302A CA 2.5 30.6 - - - -
341A CPJ 3.2 6.6 - - - +
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Residues in contact with ASN 59 (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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53A ASN* 3.0 12.5 + - - -
58A ASP* 1.3 79.8 + - - +
60A GLU* 1.3 64.4 + - - +
61A LEU* 3.3 4.7 + - - +
62A LEU* 3.7 16.0 - - + +
74A TYR* 3.8 33.1 - - + +
76A GLY 3.5 1.2 + - - -
77A ARG* 2.8 26.8 + - + +
136A GLU* 3.0 9.4 - - - +
302A CA 2.4 25.6 - - - -
341A CPJ 3.1 32.9 + - - +
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Residues in contact with GLU 60 (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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52A TYR* 3.3 28.9 + - + +
54A THR* 3.9 19.5 - - + +
57A ARG* 3.6 12.5 - - - +
58A ASP 3.2 1.8 + - - -
59A ASN* 1.3 76.6 - - - +
61A LEU* 1.3 61.7 + - - +
75A ILE* 3.4 7.1 - - - +
76A GLY* 2.8 23.3 + - - +
77A ARG* 3.0 24.8 + - - +
123A TYR* 2.6 28.4 + - - -
125A VAL* 3.3 9.9 - - + +
126A GLU* 2.9 38.4 + - - +
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Residues in contact with LEU 61 (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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30A LEU* 4.4 6.7 - - + -
33A PHE* 3.5 45.1 - - + -
35A LEU* 5.2 1.1 - - + -
50A PHE* 3.9 17.0 - - + +
51A SER 3.9 0.5 - - - -
52A TYR* 2.9 64.3 + - + +
60A GLU* 1.3 79.2 - - - +
62A LEU* 1.3 63.7 + - - +
63A VAL* 4.5 4.9 - - + -
73A LEU* 3.9 12.3 - - + -
74A TYR 3.3 5.8 - - - +
75A ILE* 4.7 2.7 - - + -
125A VAL* 4.6 6.3 - - + -
159A MET* 3.8 23.8 - - + -
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Residues in contact with LEU 62 (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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48A SER* 3.3 26.7 - - - +
50A PHE 3.3 15.7 - - - +
51A SER* 3.9 11.2 - - - -
52A TYR 5.1 0.2 - - - +
53A ASN* 6.0 0.2 - - - +
59A ASN* 3.7 15.0 - - - +
61A LEU* 1.3 76.4 - - - +
63A VAL* 1.3 68.1 + - - +
64A TYR* 4.1 10.5 - - + -
72A SER 3.6 1.2 - - - +
73A LEU* 3.4 6.7 - - - +
74A TYR* 2.8 58.8 + - + -
136A GLU* 3.6 20.4 - - - +
341A CPJ 3.7 24.7 - - + -
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Residues in contact with VAL 63 (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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35A LEU* 3.8 28.0 - - + -
37A PHE* 4.3 11.2 - - + -
49A LEU* 2.8 45.6 + - + -
50A PHE* 2.9 23.9 + - + +
61A LEU* 4.5 3.8 - - + -
62A LEU* 1.3 78.3 - - - +
64A TYR* 1.3 62.3 + - - +
71A TYR* 5.4 1.8 - - + -
72A SER 3.4 8.3 - - - +
73A LEU* 4.2 9.2 - - + -
94A ILE* 4.9 2.2 - - + -
96A VAL* 3.9 16.4 - - + -
107A PHE* 4.1 19.1 - - + -
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Residues in contact with TYR 64 (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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46A ALA* 3.4 29.8 - - + +
47A TYR* 3.5 23.3 - - - -
48A SER* 3.8 13.2 - - - -
49A LEU* 5.2 0.9 - - - -
62A LEU* 3.9 16.1 - - + -
63A VAL* 1.3 76.7 - - - +
65A LYS* 1.3 60.9 + - - +
66A GLU* 3.6 34.3 + - - -
71A TYR* 4.0 1.0 - - - -
72A SER* 2.8 39.7 + - - +
74A TYR* 3.9 23.8 - + + -
136A GLU* 4.4 0.4 - - + -
148A GLN* 3.2 42.2 + - + +
341A CPJ 4.1 17.1 + - + -
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Residues in contact with LYS 65 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43A LEU 5.8 1.0 + - - -
45A ARG 4.4 0.6 - - - +
46A ALA* 3.1 5.9 - - - +
47A TYR* 2.8 78.7 + - + +
49A LEU* 4.2 9.3 - - + +
64A TYR* 1.3 72.7 - - - +
66A GLU* 1.3 57.9 - - - +
67A ARG* 3.3 25.4 - - - +
68A VAL* 4.1 11.5 - - - +
69A GLY 4.0 1.3 - - - +
70A GLU 3.7 7.9 - - - +
71A TYR* 3.5 34.4 + - + +
86A GLU* 2.8 31.2 + - - -
88A PHE* 5.9 2.4 - - - -
92A VAL* 6.1 0.6 - - - +
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Residues in contact with GLU 66 (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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44A SER 4.8 0.2 - - - +
45A ARG* 4.4 0.3 - - - -
46A ALA* 3.3 27.3 + - - +
64A TYR* 3.7 21.3 - - - +
65A LYS* 1.3 72.1 - - - +
67A ARG* 1.3 89.8 + - + +
70A GLU* 3.7 11.1 + - + +
72A SER* 2.6 36.7 + - - +
74A TYR* 3.9 10.7 + - - -
79A LYS* 4.1 9.1 - - - +
81A THR* 4.7 10.1 - - + -
341A CPJ 6.0 0.7 - - - +
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Residues in contact with ARG 67 (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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44A SER 4.3 12.8 - - - +
45A ARG 5.4 0.7 - - - -
65A LYS* 3.3 17.7 - - - -
66A GLU* 1.3 94.7 + - - +
68A VAL* 1.3 72.5 + - - +
70A GLU* 2.8 65.1 + - - +
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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