Contacts of the strand formed by residues 76 - 85 (chain A) in PDB entry 4QAE
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 CYS 76 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70A MET 3.7 0.4 - - - +
75A LYS* 1.3 87.0 - - - +
77A GLU* 1.3 60.4 + - - +
78A TYR* 3.6 33.5 - - + +
175A CYS* 2.0 57.9 - - + -
14R CYS* 3.4 30.3 - - - -
15R HIS* 3.7 10.0 - - - -
21R MET* 4.2 6.2 + - - +
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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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68A ILE 3.4 0.9 - - - +
69A VAL* 3.4 5.7 - - - +
70A MET* 2.8 48.0 + - + +
72A LEU* 3.6 29.3 - - + +
75A LYS* 3.8 19.5 + - - +
76A CYS* 1.3 72.4 - - - +
78A TYR* 1.3 64.7 + - - +
79A LEU* 3.7 31.4 - - + +
75B LYS* 2.7 35.0 + - - +
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Residues in contact with TYR 78 (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 THR* 4.5 4.5 - - + -
68A ILE 3.2 5.4 - - - +
69A VAL* 3.8 29.6 - - + -
76A CYS* 3.6 21.4 - - + +
77A GLU* 1.3 78.7 + - - +
79A LEU* 1.3 69.4 + - - +
80A PHE* 3.5 30.2 - - + -
175A CYS 4.6 3.5 + - - -
127C TRP* 4.6 0.7 - - - -
14R CYS* 3.6 18.4 - - - +
21R MET* 3.7 19.7 - - + -
22R CYS* 3.6 6.6 - - - -
23R CYS* 3.2 62.1 + - + -
25R THR* 4.0 8.5 - - + -
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Residues in contact with LEU 79 (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 THR* 3.5 4.7 - - - +
68A ILE* 2.7 46.5 + - + +
70A MET* 4.6 8.3 - - - -
77A GLU* 3.7 30.5 - - + +
78A TYR* 1.3 83.2 - - - +
80A PHE* 1.3 66.6 + - - +
75B LYS* 5.7 1.3 - - - +
9P PHE* 3.7 33.0 - - + -
20P GLY* 3.9 15.7 - - - -
21P MET* 4.0 30.7 - - + +
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Residues in contact with PHE 80 (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 VAL 3.3 2.2 - - - +
67A THR* 3.7 27.8 - - + -
78A TYR* 3.5 34.5 - + + -
79A LEU* 1.3 78.6 - - - +
81A GLN* 1.3 69.6 + - - +
21P MET* 5.1 10.3 - - - +
3R HIS* 3.6 27.1 - + + -
5R PRO* 3.7 40.2 - - + -
7R CYS* 5.5 0.2 - - - -
23R CYS* 5.1 4.0 - - + -
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Residues in contact with GLN 81 (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 ASN* 3.8 2.3 - - - +
66A VAL* 2.9 35.8 + - + +
68A ILE* 3.3 23.7 - - + +
80A PHE* 1.3 80.7 - - - +
82A THR* 1.3 65.4 + - - +
83A PHE* 3.3 31.9 - - + -
94A LEU* 3.8 30.6 - - + +
123A PHE* 5.6 1.0 - - - -
134A TRP* 6.2 0.2 - - - -
9P PHE* 3.4 41.8 + - + +
21P MET* 5.9 0.7 - - + -
3R HIS* 5.9 0.3 - - - -
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Residues in contact with THR 82 (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 SER* 4.5 9.9 - - - +
64A TYR 3.5 9.6 - - - +
65A ASN* 4.0 14.7 + - - +
81A GLN* 1.3 76.6 + - - +
83A PHE* 1.3 63.2 + - - +
84A VAL* 3.9 20.6 - - + -
94A LEU* 3.5 6.2 - - - +
95A GLY* 2.9 37.1 + - - +
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Residues in contact with PHE 83 (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 THR* 5.6 1.3 - - + -
56A TYR* 3.6 37.5 - + - -
63A SER* 3.2 5.8 - - - -
64A TYR* 2.9 44.5 + + + +
66A VAL* 3.6 22.4 - - + -
81A GLN* 3.3 33.4 - - + -
82A THR* 1.3 74.6 - - - +
84A VAL* 1.3 60.7 + - - +
92A PHE* 3.7 21.3 - + + -
93A THR 3.4 3.4 - - - -
94A LEU* 3.4 30.5 - - + -
108A VAL* 3.9 22.2 - - + -
123A PHE* 3.9 18.8 - + - -
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Residues in contact with VAL 84 (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 SER* 4.3 5.6 - - - -
82A THR* 3.9 20.4 - - + -
83A PHE* 1.3 74.7 - - - +
85A PRO* 1.4 78.2 - - + +
86A GLY 3.2 0.3 + - - -
92A PHE* 3.2 3.4 - - - -
93A THR* 2.8 57.9 + - - +
95A GLY* 4.0 3.4 - - - -
96A GLY* 3.0 34.1 - - - +
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Residues in contact with PRO 85 (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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61A ASP* 4.1 6.1 - - - +
62A LYS* 3.4 39.0 - - + +
63A SER* 3.8 10.5 - - - +
83A PHE 4.1 0.2 - - - +
84A VAL* 1.4 90.2 - - + +
86A GLY* 1.3 65.6 + - - +
91A GLU 3.9 1.1 - - - +
92A PHE* 3.7 12.7 - - + -
93A THR* 4.9 0.7 + - - -
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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