Contacts of the strand formed by residues 57 - 67 (chain S) 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 S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53S ASN* 3.6 7.9 - - - -
54S THR* 2.8 42.7 + - - +
55S GLN 3.2 6.0 + - - +
56S GLY* 1.3 83.1 - - - +
58S ASP* 1.3 62.1 + - - +
60S GLU* 3.4 18.7 + - - +
77S ARG* 3.3 27.5 - - - +
123S TYR* 3.0 28.5 + - - -
124S PHE 4.6 2.8 + - - -
126S GLU* 3.3 43.9 + - - +
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Residues in contact with ASP 58 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348M CPJ 3.2 6.8 - - - +
53S ASN* 2.9 14.0 + - - +
56S GLY 4.2 1.0 + - - -
57S ARG* 1.3 71.8 - - - +
59S ASN* 1.3 77.9 + - - +
60S GLU 3.2 0.7 + - - -
77S ARG* 3.2 32.9 + - + +
137S GLN 2.8 12.0 - - - +
138S ASP* 3.4 20.0 - - - +
337S CA 2.5 30.6 - - - -
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Residues in contact with ASN 59 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348M CPJ 2.9 37.1 + - - +
53S ASN* 3.1 9.1 + - - -
58S ASP* 1.3 80.2 + - - +
60S GLU* 1.3 63.4 + - - +
61S LEU* 3.3 3.5 + - - +
62S LEU* 4.0 16.4 - - + -
74S TYR* 3.9 28.9 - - + +
76S GLY 3.6 1.2 + - - -
77S ARG* 2.8 28.7 + - + +
136S GLU* 3.1 8.3 - - - +
337S CA 2.4 25.8 - - - -
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Residues in contact with GLU 60 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52S TYR* 3.5 20.0 + - + +
53S ASN* 4.0 0.2 + - - -
54S THR* 3.8 25.6 - - + +
57S ARG* 3.4 23.4 - - - +
58S ASP 3.2 1.8 + - - -
59S ASN* 1.3 76.6 - - - +
61S LEU* 1.3 60.7 + - - +
75S ILE* 3.4 5.4 - - - +
76S GLY* 2.9 20.5 + - - +
77S ARG* 3.1 16.5 + - - -
123S TYR* 2.6 30.9 + - - -
125S VAL* 3.2 14.1 - - + +
126S GLU* 2.9 27.5 + - - +
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Residues in contact with LEU 61 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30S LEU* 4.3 5.6 - - + -
33S PHE* 3.3 46.2 - - + -
35S LEU* 5.7 0.9 - - + -
50S PHE* 3.9 12.2 - - + +
52S TYR* 3.0 60.9 + - + +
60S GLU* 1.3 78.6 - - - +
62S LEU* 1.3 65.6 + - - +
63S VAL* 5.1 2.5 - - + -
73S LEU* 3.7 15.3 - - + -
74S TYR 3.2 4.5 - - - -
75S ILE* 4.2 2.9 - - + -
125S VAL* 4.4 7.4 - - + -
159S MET* 3.8 25.4 - - + -
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Residues in contact with LEU 62 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348M CPJ 3.5 31.6 - - + -
48S SER* 3.4 21.8 - - - +
50S PHE 3.3 16.8 - - - +
51S SER* 4.0 7.9 - - - -
52S TYR 5.2 0.4 - - - +
53S ASN* 6.0 0.2 - - - +
59S ASN* 4.0 13.9 - - - +
61S LEU* 1.3 76.9 - - - +
63S VAL* 1.3 70.8 + - - +
64S TYR* 4.1 4.9 - - + -
72S SER 3.6 1.2 - - - +
73S LEU* 3.3 5.7 - - - -
74S TYR* 2.7 64.5 + - + -
136S GLU* 3.7 21.1 - - + +
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Residues in contact with VAL 63 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35S LEU* 3.9 28.0 - - + -
37S PHE* 4.2 9.0 - - + -
48S SER 3.9 0.7 - - - -
49S LEU* 2.9 47.5 + - + +
50S PHE* 2.9 24.7 + - + +
61S LEU* 5.1 2.0 - - + -
62S LEU* 1.3 76.6 - - - +
64S TYR* 1.3 61.4 + - - +
71S TYR* 5.4 2.7 - - + -
72S SER 3.5 7.4 - - - +
73S LEU* 4.3 8.7 - - + -
94S ILE* 4.9 3.4 - - + -
96S VAL* 3.9 16.6 - - + -
107S PHE* 4.3 17.3 - - + -
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Residues in contact with TYR 64 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348M CPJ 3.9 26.6 - - + -
46S ALA* 3.5 32.1 - - + +
47S TYR 3.7 18.4 - - - -
48S SER* 3.9 11.7 - - - -
49S LEU* 5.2 0.7 - - - -
62S LEU* 3.8 8.9 + - + -
63S VAL* 1.3 75.8 - - - +
65S LYS* 1.3 60.6 + - - +
66S GLU* 3.6 29.2 + - + -
71S TYR* 4.0 1.5 - - - +
72S SER* 2.8 40.9 + - - +
74S TYR* 3.9 26.2 - + + -
136S GLU* 4.4 2.2 - - + -
148S GLN* 3.2 40.7 + - + +
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Residues in contact with LYS 65 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43S LEU 6.0 0.2 + - - -
45S ARG 4.4 0.9 - - - +
46S ALA* 3.1 4.3 - - - -
47S TYR* 2.9 77.3 + - + +
49S LEU* 4.2 9.1 - - + +
63S VAL 4.4 0.2 - - - -
64S TYR* 1.3 72.5 - - - +
66S GLU* 1.3 61.1 + - - +
67S ARG 3.2 24.9 + - - +
68S VAL* 4.0 9.5 - - - +
69S GLY 3.9 2.0 - - - +
70S GLU 3.6 9.4 - - - +
71S TYR* 3.3 35.7 + - + +
86S GLU* 3.0 28.1 + - - -
88S PHE* 6.0 1.4 - - - -
92S VAL* 6.2 0.2 - - - +
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Residues in contact with GLU 66 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44S SER 4.7 0.3 - - - +
45S ARG 4.4 0.2 - - - -
46S ALA* 3.4 28.1 + - + +
64S TYR* 3.6 20.0 - - + +
65S LYS* 1.3 73.2 - - - +
67S ARG* 1.3 86.8 + - + +
70S GLU* 3.7 16.3 + - + +
72S SER* 2.8 35.9 + - - +
74S TYR* 3.8 11.3 + - - -
79S LYS* 3.9 19.9 + - - +
81S THR* 4.5 3.0 - - + +
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Residues in contact with ARG 67 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44S SER 4.3 13.2 - - - +
45S ARG 5.4 0.7 - - - -
65S LYS* 3.2 18.3 - - - -
66S GLU* 1.3 93.8 + - - +
68S VAL* 1.3 77.7 + - - +
70S GLU* 2.9 54.9 + - - +
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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