Contacts of the strand formed by residues 64 - 75 (chain A) in PDB entry 5X1X
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 VAL 64 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47A LYS* 3.4 40.6 - - - +
50A LEU* 5.0 4.3 - - + -
51A ILE* 5.5 2.9 - - + +
54A ILE* 4.9 12.3 - - + -
62A LEU 4.1 5.8 + - - +
63A ILE* 1.3 91.5 - - - +
65A GLY* 1.3 70.9 + - - +
85A TYR* 3.7 24.5 - - + -
86A LYS 3.4 10.3 - - - +
87A CYS* 4.6 12.1 - - - -
88A THR* 4.8 1.6 - - - -
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Residues in contact with GLY 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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64A VAL* 1.3 79.6 - - - +
66A ASP* 1.3 69.7 + - - +
86A LYS* 2.7 20.2 + - - -
88A THR* 5.0 2.1 + - - -
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Residues in contact with ASP 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 VAL* 4.4 0.4 - - - +
65A GLY* 1.3 81.3 - - - +
67A LYS* 1.3 71.1 + - - +
68A VAL* 3.4 0.9 + - - +
85A TYR* 3.7 10.1 - - - -
86A LYS* 3.4 29.2 + - + +
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Residues in contact with LYS 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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46A GLU* 3.5 18.4 + - - -
66A ASP* 1.3 82.0 + - - +
68A VAL* 1.3 65.8 - - - +
69A ILE* 4.1 9.2 - - - +
70A THR* 2.9 26.9 + - - +
83A THR* 2.9 23.8 - - - +
85A TYR* 3.2 47.6 + - + +
125A LYS* 3.9 7.8 + - - -
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Residues in contact with VAL 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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11A ILE* 3.5 16.8 - - + -
67A LYS* 1.3 74.9 - - - +
69A ILE* 1.3 62.5 + - + +
84A THR* 3.0 43.3 + - - +
86A LYS* 3.5 31.2 - - + +
122A ALA* 3.4 28.0 - - + +
125A LYS* 2.9 42.1 + - + +
126A ILE* 5.5 1.3 - - + -
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Residues in contact with ILE 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 LYS* 3.8 5.7 - - - +
68A VAL* 1.3 84.5 - - + +
70A THR* 1.3 77.7 + - - +
71A THR* 4.0 12.5 + - - +
83A THR* 3.0 27.2 + - - -
84A THR* 3.8 1.3 + - - +
121A PRO* 4.4 19.5 - - + +
122A ALA* 3.2 38.4 - - + +
125A LYS* 5.1 5.4 - - + -
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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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46A GLU* 5.7 4.9 - - - +
67A LYS* 2.9 31.7 + - - +
69A ILE* 1.3 82.8 - - - +
71A THR* 1.3 66.4 + - - +
72A GLU* 3.6 27.1 - - + +
81A ARG* 5.8 2.9 - - + -
82A LEU 4.4 1.3 - - - +
83A THR* 4.5 4.3 - - - +
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Residues in contact with THR 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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69A ILE* 4.0 12.1 - - - +
70A THR* 1.3 76.8 - - - +
72A GLU* 1.3 66.7 + - - +
73A HIS* 3.6 13.9 - - + +
81A ARG* 3.1 6.1 - - - +
82A LEU 2.9 39.3 + - - +
117A PRO 4.3 0.9 - - - +
118A ALA* 2.7 45.6 + - - +
121A PRO* 4.3 11.9 - - + +
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Residues in contact with GLU 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* 3.6 22.0 - - + +
71A THR* 1.3 84.7 - - - +
73A HIS* 1.3 73.5 + - - +
79A ILE* 4.3 5.9 - - + +
80A VAL 3.4 7.2 - - - +
81A ARG* 3.5 52.2 + - + -
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Residues in contact with HIS 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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71A THR* 3.6 20.2 - - + +
72A GLU* 1.3 98.8 + - - +
74A GLU* 1.3 61.8 + - - +
75A TYR* 3.5 8.7 + + + -
79A ILE* 3.4 10.8 - - - +
80A VAL* 3.0 48.9 + - + -
117A PRO* 4.0 31.5 - - + +
118A ALA* 3.6 22.8 - - + +
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Residues in contact with GLU 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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2A LYS* 3.3 25.9 + - - +
73A HIS* 1.3 72.0 - - - +
75A TYR* 1.3 71.5 + - - +
76A ASP* 5.6 0.3 - - - +
79A ILE* 3.1 32.6 - - - +
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Residues in contact with TYR 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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2A LYS* 3.6 11.6 + - - -
5A ILE* 6.0 3.1 - - + -
28A SER* 5.2 10.9 + - - -
73A HIS* 3.5 8.2 + - + -
74A GLU* 1.3 90.8 - - - +
76A ASP* 1.3 65.6 + - - +
77A PHE* 4.1 10.1 - + + +
78A GLY 2.6 37.3 + - - +
79A ILE 4.9 0.2 - - - -
80A VAL* 3.6 40.3 - - + +
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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