Contacts of the strand formed by residues 57 - 67 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53G ASN* 3.6 7.6 - - - -
54G THR* 2.8 47.7 + - - +
55G GLN 3.7 8.1 - - - +
56G GLY* 1.3 83.3 - - - +
58G ASP* 1.3 62.2 + - - +
60G GLU* 3.4 9.0 + - + +
77G ARG* 3.4 29.3 - - - +
123G TYR* 2.8 41.2 + - - -
124G PHE 4.5 2.0 + - - -
126G GLU* 3.5 32.5 + - + +
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Residues in contact with ASP 58 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344D CPJ 3.3 6.6 - - - +
53G ASN* 3.0 13.6 + - - +
56G GLY 4.1 1.8 + - - -
57G ARG* 1.3 72.7 - - - +
59G ASN* 1.3 78.2 + - - +
60G GLU 3.2 0.2 - - - -
77G ARG* 2.8 34.4 + - + +
137G GLN 2.9 11.1 - - - +
138G ASP* 3.3 20.5 - - - +
313G CA 2.4 31.3 - - - -
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Residues in contact with ASN 59 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344D CPJ 2.9 36.5 + - - +
52G TYR 4.6 0.2 - - - -
53G ASN* 3.1 9.8 + - - -
58G ASP* 1.3 79.8 + - - +
60G GLU* 1.3 63.7 + - - +
61G LEU* 3.3 4.4 + - - +
62G LEU* 3.9 16.3 - - + +
74G TYR* 4.0 24.9 - - + +
76G GLY 3.6 0.5 + - - -
77G ARG* 2.9 31.1 + - + +
136G GLU* 2.9 8.5 - - - +
313G CA 2.3 27.8 - - - -
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Residues in contact with GLU 60 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52G TYR* 3.3 21.5 + - + +
53G ASN* 4.1 0.4 + - - -
54G THR* 3.9 16.8 - - - +
57G ARG* 3.4 16.8 + - - +
58G ASP 3.1 2.5 + - - -
59G ASN* 1.3 76.6 - - - +
61G LEU* 1.3 60.4 + - - +
74G TYR 4.1 0.2 - - - -
75G ILE* 3.4 7.8 - - - +
76G GLY* 2.8 21.2 + - - +
77G ARG* 3.1 16.2 + - - +
123G TYR* 2.7 29.9 + - - -
125G VAL* 3.1 18.7 - - + +
126G GLU* 2.7 36.9 + - - +
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Residues in contact with LEU 61 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30G LEU* 4.5 0.7 - - + -
33G PHE* 3.5 46.2 - - + -
35G LEU* 5.5 0.4 - - + -
50G PHE* 3.9 13.9 - - + +
52G TYR* 2.9 61.0 + - + +
60G GLU* 1.3 78.4 - - - +
62G LEU* 1.3 67.4 + - - +
63G VAL* 4.8 3.4 - - + -
73G LEU* 3.7 14.1 - - + -
74G TYR 3.2 4.9 - - - +
75G ILE* 4.3 2.5 - - + -
125G VAL* 4.5 11.2 - - + -
159G MET* 3.7 25.1 - - + -
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Residues in contact with LEU 62 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344D CPJ 3.5 26.0 - - + -
48G SER* 3.3 28.3 - - - +
50G PHE 3.3 12.1 - - - +
51G SER* 4.1 6.3 - - - -
52G TYR 5.2 0.2 - - - +
53G ASN* 6.0 0.2 - - - +
59G ASN* 3.8 15.7 - - - +
61G LEU* 1.3 78.3 - - - +
63G VAL* 1.3 70.5 + - - +
64G TYR* 4.1 6.7 - - + -
72G SER 3.6 1.2 - - - +
73G LEU* 3.3 7.1 - - - +
74G TYR* 2.8 59.9 + - + -
136G GLU* 3.4 29.4 - - + +
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Residues in contact with VAL 63 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35G LEU* 3.8 27.4 - - + -
37G PHE* 4.3 9.0 - - + -
49G LEU* 2.8 46.4 + - + -
50G PHE* 2.9 21.6 + - + -
61G LEU* 4.8 1.8 - - + -
62G LEU* 1.3 80.2 - - - +
64G TYR* 1.3 62.6 + - - +
71G TYR* 5.3 2.9 - - + -
72G SER 3.5 8.1 - - - +
73G LEU* 4.3 9.2 - - + -
94G ILE* 5.0 3.6 - - + -
96G VAL* 3.9 17.5 - - + -
107G PHE* 4.2 17.7 - - + -
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Residues in contact with TYR 64 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344D CPJ 4.0 24.6 - - + -
46G ALA* 3.4 26.6 - - + +
47G TYR* 3.5 21.3 - - - -
48G SER* 3.8 15.5 - - - -
49G LEU* 4.9 2.7 - - - -
62G LEU* 4.1 7.0 - - + -
63G VAL* 1.3 76.4 - - - +
65G LYS* 1.3 61.3 + - - +
66G GLU* 3.6 34.0 + - + -
71G TYR* 3.8 2.0 - - - +
72G SER* 2.8 36.4 + - - +
74G TYR* 3.9 31.4 - + + -
136G GLU* 4.7 0.7 - - + -
148G GLN* 3.1 38.7 + - + +
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Residues in contact with LYS 65 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43G LEU 5.9 0.6 + - - -
45G ARG 4.4 0.6 - - - +
46G ALA* 3.2 1.6 - - - -
47G TYR* 2.8 79.0 + - + +
49G LEU* 4.0 8.7 - - + +
63G VAL 4.3 0.4 - - - -
64G TYR* 1.3 72.0 - - - +
66G GLU* 1.3 62.2 + - - +
67G ARG* 3.4 22.4 - - - +
68G VAL* 4.0 12.5 - - - +
69G GLY 3.9 1.6 - - - +
70G GLU 3.8 8.3 - - - +
71G TYR* 3.5 35.2 + - + +
86G GLU* 2.9 30.0 + - - -
88G PHE* 6.0 1.4 - - - -
92G VAL* 6.3 0.2 - - - +
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Residues in contact with GLU 66 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344D CPJ 6.1 1.5 - - - +
44G SER 4.9 0.3 - - - +
45G ARG 4.4 0.2 - - - -
46G ALA* 3.4 33.2 + - - +
64G TYR* 3.6 24.7 + - + -
65G LYS* 1.3 72.5 - - - +
67G ARG* 1.3 93.1 + - + +
70G GLU* 3.7 13.6 + - + +
72G SER* 4.2 15.9 - - - +
74G TYR* 5.5 1.6 + - - +
79G LYS* 4.2 18.1 + - - +
81G THR* 5.7 1.6 - - + -
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Residues in contact with ARG 67 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44G SER 4.5 11.9 - - - +
45G ARG 5.5 0.9 - - - -
46G ALA* 5.5 0.2 - - - +
65G LYS* 3.4 12.8 - - - -
66G GLU* 1.3 101.0 + - - +
68G VAL* 1.3 73.5 + - - +
69G GLY 3.3 0.3 + - - -
70G GLU* 3.1 62.6 + - - +
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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