Contacts of the strand formed by residues 59 - 73 (chain A) in PDB entry 2I69
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 TYR 59 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57A ARG* 3.2 20.1 + - + -
58A SER* 1.3 76.9 - - - +
60A CYS* 1.3 62.5 + - - +
61A TYR* 3.7 0.3 + - - -
124A LYS* 3.4 1.4 - - - -
125A ALA* 2.8 41.2 + - + +
204A MET* 5.6 0.9 - - + -
218A PHE* 2.8 67.0 + + - -
219A MET* 3.0 20.8 + - - -
221A LEU* 3.6 32.8 + - + -
223A LEU* 3.9 24.5 - - + -
224A PRO 3.3 7.2 - - - -
225A TRP* 3.5 25.1 - + + -
233A TRP* 3.8 4.8 - - - -
262A LEU* 6.5 0.2 - - + -
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Residues in contact with CYS 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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59A TYR* 1.3 72.5 - - - +
61A TYR* 1.3 59.8 + - - +
62A LEU 3.5 16.4 - - - -
63A ALA* 4.5 1.8 - - - -
119A PHE* 4.0 11.9 - - + -
121A CYS* 2.1 57.2 - - - -
223A LEU* 3.3 19.1 - - - +
224A PRO* 2.8 25.2 + - + +
233A TRP* 3.4 14.5 - - + -
239A LEU* 3.5 11.3 - - + +
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Residues in contact with TYR 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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59A TYR 4.6 0.2 - - - -
60A CYS* 1.3 76.5 - - - +
62A LEU* 1.3 64.2 + - + +
63A ALA 4.3 0.2 - - - -
123A THR* 3.1 36.6 + - - +
124A LYS* 3.1 38.3 + - - -
125A ALA* 3.9 12.1 - - + -
206A VAL* 3.9 11.9 - - + -
207A GLY* 3.4 24.0 + - - -
223A LEU* 4.5 1.1 - - + -
239A LEU* 4.0 6.6 - - - +
257A SER* 3.8 6.4 - - - -
258A GLN* 3.0 47.1 + - + +
259A GLU* 3.3 48.0 + - + -
262A LEU* 3.9 18.2 - - + -
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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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60A CYS* 3.5 7.5 - - - -
61A TYR* 1.3 80.3 - - + +
63A ALA* 1.3 69.1 + - - +
122A SER* 2.7 53.3 + - - +
123A THR* 3.5 17.6 + - - +
239A LEU* 5.0 0.9 - - - -
255A LEU 4.1 3.1 - - - +
256A GLY* 3.9 8.1 - - - -
257A SER* 3.5 40.6 - - - +
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Residues in contact with ALA 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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60A CYS* 4.5 0.7 - - - -
61A TYR 4.3 0.4 + - - -
62A LEU* 1.3 89.3 - - - +
64A THR* 1.3 67.8 + - - +
65A VAL* 5.7 1.1 - - + -
119A PHE* 3.5 28.7 - - + -
120A ALA 3.2 12.8 - - - +
121A CYS* 4.5 0.2 - - - +
122A SER* 4.3 1.8 - - - +
239A LEU* 4.4 20.7 - - + +
240A MET* 6.1 0.2 - - + -
254A ALA* 3.6 19.3 - - + +
255A LEU 4.5 4.0 + - - -
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Residues in contact with THR 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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63A ALA* 1.3 77.1 + - - +
65A VAL* 1.3 74.8 + - - +
66A SER* 4.1 9.1 + - - -
118A LYS 3.4 3.5 - - - +
119A PHE* 3.6 4.0 - - - -
120A ALA* 2.8 52.2 + - + +
122A SER* 3.4 16.8 + - - -
254A ALA* 4.3 1.8 - - - -
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Residues in contact with VAL 65 (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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63A ALA* 5.7 1.3 - - + -
64A THR* 1.3 78.7 - - - +
66A SER* 1.3 64.6 + - - +
68A LEU* 4.2 7.7 - - + +
117A ALA* 3.9 12.6 - - + -
118A LYS 3.3 3.1 - - - +
119A PHE* 5.6 0.4 - - + -
240A MET* 3.3 27.6 - - + -
252A VAL* 3.3 41.2 - - + +
253A ILE* 3.5 19.5 - - - +
254A ALA* 3.5 25.0 - - + +
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Residues in contact with SER 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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64A THR* 4.8 10.8 + - - +
65A VAL* 1.3 75.4 - - - +
67A ASP* 1.3 80.3 + - - +
68A LEU* 3.6 5.2 - - - -
117A ALA* 3.6 1.7 - - - -
118A LYS* 2.6 69.6 + - - +
120A ALA* 5.8 0.5 - - - +
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Residues in contact with ASP 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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66A SER* 1.3 95.7 + - - +
68A LEU* 1.3 65.4 + - - +
69A SER* 3.6 2.6 + - - -
84A LYS* 6.4 0.2 - - - -
90A PHE* 3.2 31.2 - - + -
117A ALA* 3.6 3.5 - - - -
118A LYS* 4.2 10.0 + - - +
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Residues in contact with LEU 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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65A VAL* 4.2 11.0 - - + +
66A SER* 4.1 6.3 - - - +
67A ASP* 1.3 83.9 - - - +
69A SER* 1.3 60.3 + - - +
115A THR* 5.7 0.7 - - + -
116A CYS 3.5 8.3 - - - +
117A ALA* 4.3 4.5 - - + -
249A LYS* 3.7 24.9 + - + +
250A GLN 4.1 10.5 - - - +
251A SER* 4.3 2.7 - - - +
252A VAL* 3.3 56.1 - - + +
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Residues in contact with SER 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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67A ASP 3.6 2.9 + - - -
68A LEU* 1.3 75.0 - - - +
70A THR* 1.3 65.5 + - - +
82A ASN* 2.7 28.8 + - - -
84A LYS* 4.2 13.8 - - - +
115A THR* 3.7 4.8 - - - +
116A CYS 3.0 31.7 + - - +
249A LYS* 5.0 0.4 - - - +
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Residues in contact with THR 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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69A SER* 1.3 79.1 - - - +
71A LYS* 1.3 65.0 + - - +
72A ALA* 3.9 2.8 + - - +
82A ASN* 4.0 0.4 - - - -
113A ILE* 4.0 14.0 - - - +
114A ASP 3.5 7.3 + - - -
115A THR* 3.4 23.6 + - - -
246A HIS 5.3 0.3 + - - -
247A ALA 5.0 0.2 + - - -
248A THR 3.0 31.0 + - - +
249A LYS* 4.0 14.1 - - - +
250A GLN* 3.9 18.0 + - - +
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Residues in contact with LYS 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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70A THR* 1.3 73.8 - - - +
72A ALA* 1.3 66.8 + - - +
80A ALA* 3.7 15.4 - - + +
81A HIS 4.5 12.1 + - - +
82A ASN* 3.5 32.2 - - + +
83A ASP* 4.9 11.2 + - - +
113A ILE* 3.4 3.3 - - - +
114A ASP 2.9 33.6 + - - +
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Residues in contact with ALA 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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70A THR 3.9 4.1 + - - +
71A LYS* 1.3 83.7 - - - +
73A ALA* 1.3 61.2 + - - +
80A ALA* 4.2 1.6 - - - -
99A ARG* 3.7 18.4 - - - +
112A SER 3.7 4.3 - - - -
113A ILE* 4.1 7.2 - - + -
247A ALA 3.6 23.8 - - - +
248A THR* 5.5 1.1 - - - +
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Residues in contact with ALA 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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72A ALA* 1.3 76.7 - - - +
74A CYS* 1.3 65.1 + - - +
77A MET* 4.6 7.6 - - + +
78A GLY 3.4 23.3 - - - +
79A GLU 4.6 0.2 - - - -
80A ALA* 3.6 21.5 - - + +
99A ARG* 4.4 3.4 - - - -
111A GLY* 3.2 3.5 - - - -
112A SER* 2.8 39.9 + - - +
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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