Contacts of the strand formed by residues 67 - 78 (chain A) in PDB entry 1SY2
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 THR 67 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58A TYR* 3.7 30.7 - - + +
59A HIS 3.4 5.2 - - - +
60A TYR* 3.1 15.0 - - + -
65A GLN 2.8 16.3 + - - -
66A ASP* 1.3 76.3 + - - +
68A PHE* 1.3 74.2 + - - +
69A TYR* 4.6 9.4 - - + -
96A LYS* 5.9 1.0 + - - -
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Residues in contact with PHE 68 (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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40A TYR* 3.4 19.1 - - - -
58A TYR* 3.6 2.8 - - - -
59A HIS* 3.0 66.1 + + + +
66A ASP* 3.5 22.4 - - - -
67A THR* 1.3 81.8 - - - +
69A TYR* 1.3 64.9 + - - +
70A ASP* 3.5 17.7 - - - +
88A LYS* 3.9 32.3 - - + +
89A VAL 5.3 0.2 - - - -
125A LYS* 6.0 0.7 - - - -
185A HEM 3.7 50.3 - + + -
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Residues in contact with TYR 69 (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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57A LEU 3.2 15.9 - - - +
58A TYR* 3.4 39.6 - + + -
67A THR* 4.6 7.4 - - + -
68A PHE* 1.3 77.3 - - - +
70A ASP* 1.3 71.3 + - - +
88A LYS* 3.5 6.4 - - - +
89A VAL* 3.0 44.9 + - + +
90A ASP* 4.2 2.2 - - - +
91A LYS* 3.6 31.6 - - + +
174A ASP* 3.6 27.6 + - - +
177A SER* 4.1 10.2 - - - -
178A LEU* 4.3 9.4 - - + -
181A LEU* 3.5 22.7 - - + -
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Residues in contact with ASP 70 (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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55A GLU 4.6 0.2 - - - -
56A ALA* 3.2 5.9 - - - +
57A LEU* 2.8 50.8 + - + +
59A HIS* 4.7 0.7 + - - -
68A PHE* 3.5 13.3 - - - +
69A TYR* 1.3 79.2 - - - +
71A VAL* 1.3 62.4 + - - +
72A SER* 5.5 0.2 - - - +
86A PHE* 3.6 17.3 - - + -
87A LYS 3.2 14.8 - - - +
88A LYS* 3.5 3.1 - - - -
89A VAL* 4.2 5.1 - - - +
181A LEU* 4.7 1.6 - - - +
185A HEM 2.5 48.3 - - - +
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Residues in contact with VAL 71 (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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54A LYS* 3.6 17.5 - - - -
55A GLU 3.4 10.5 - - - +
56A ALA* 4.8 2.5 - - + -
57A LEU* 6.4 0.2 - - - -
70A ASP* 1.3 75.2 - - - +
72A SER* 1.3 67.3 + - - +
85A ASN 4.2 0.5 - - - +
87A LYS* 2.9 64.8 + - + +
89A VAL* 3.7 17.7 - - + -
99A VAL* 5.4 0.2 - - - +
181A LEU* 3.7 18.4 - - + +
182A LEU* 5.1 0.7 - - - +
184A LYS* 3.5 26.7 - - + +
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Residues in contact with SER 72 (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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54A LYS* 3.3 13.5 - - - -
55A GLU 2.9 33.4 + - - +
57A LEU* 5.7 0.7 - - - +
70A ASP* 5.5 0.5 - - - +
71A VAL* 1.3 72.6 - - - +
73A GLU* 1.4 57.5 + - - +
74A LEU* 3.8 6.6 + - - +
84A ALA* 3.8 21.3 - - - -
85A ASN 3.4 14.0 + - - -
86A PHE* 3.2 28.8 + - - +
105A TYR* 3.8 13.4 + - - -
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Residues in contact with GLU 73 (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 LYS* 3.8 38.9 - - + +
53A LEU 3.3 17.1 + - - +
54A LYS* 3.9 10.5 - - + +
72A SER* 1.4 71.2 - - - +
74A LEU* 1.3 69.5 + - - +
75A GLN* 3.7 15.1 + - + +
83A THR 4.4 2.4 - - - +
84A ALA* 5.1 0.2 - - - -
85A ASN* 4.4 9.5 + - - +
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Residues in contact with LEU 74 (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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18A PHE* 3.8 29.2 - - + -
53A LEU* 2.9 34.6 + - + +
54A LYS 5.1 0.4 - - - -
55A GLU* 3.8 35.4 - - + +
72A SER* 4.0 14.4 - - - +
73A GLU* 1.3 82.3 - - - +
75A GLN* 1.3 62.5 + - - +
76A VAL* 5.2 1.7 - - - +
82A TYR* 3.7 31.2 - - + -
83A THR 3.6 4.3 - - - -
84A ALA* 3.7 25.4 - - + -
107A PHE* 5.0 2.7 - - + -
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Residues in contact with GLN 75 (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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73A GLU* 4.4 12.8 + - + +
74A LEU* 1.3 77.6 - - - +
76A VAL* 1.3 63.4 + - - +
77A GLU* 4.3 9.8 - - - +
82A TYR* 3.2 8.5 - - - +
83A THR* 2.9 45.0 + - - +
85A ASN* 3.6 26.9 - - - +
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Residues in contact with VAL 76 (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 LEU* 4.5 11.0 - - + -
74A LEU 5.2 1.3 - - - +
75A GLN* 1.3 75.5 - - - +
77A GLU* 1.3 69.3 + - - +
78A SER* 3.7 25.4 - - - +
79A LEU* 5.3 1.3 - - - -
82A TYR* 3.9 22.7 - - + -
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Residues in contact with GLU 77 (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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75A GLN* 4.3 7.1 - - - +
76A VAL* 1.3 80.9 - - - +
78A SER* 1.3 64.5 + - - +
81A LYS* 2.9 25.3 + - + +
82A TYR 4.4 2.2 - - - +
83A THR* 2.6 39.4 + - - +
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Residues in contact with SER 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A VAL* 3.7 14.7 - - - +
77A GLU* 1.3 80.4 - - - +
79A LEU* 1.3 70.9 + - - +
80A GLY 3.0 1.0 + - - -
81A LYS* 3.0 43.2 + - - +
82A TYR* 4.4 1.0 - - - -
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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