Contacts of the strand formed by residues 74 - 85 (chain A) in PDB entry 1XWD
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 PHE 74 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A PHE* 4.4 23.8 - + + -
69A THR* 3.4 4.2 - - - +
70A VAL* 3.3 37.7 + - + +
71A MET* 5.1 3.1 - - + -
72A GLY* 3.3 38.1 - - - -
73A GLY* 1.3 79.0 - - - +
75A LYS* 1.3 60.3 + - - +
76A VAL* 4.7 0.7 - - + -
39B TYR* 4.0 35.2 - + + -
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Residues in contact with LYS 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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67A ARG* 4.4 31.0 - - + +
68A VAL 3.9 6.3 - - - +
69A THR* 4.0 18.3 + - + +
73A GLY 4.0 2.2 + - - -
74A PHE* 1.3 72.8 - - - +
76A VAL* 1.3 68.8 + - - +
38B VAL 4.6 0.7 - - - +
39B TYR* 4.0 12.2 - - - -
40B LYS 5.4 0.7 + - - -
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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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18A PHE* 3.9 27.1 - - + -
25A ILE* 4.6 11.4 - - + -
67A ARG* 3.4 5.6 - - - -
68A VAL* 2.9 49.4 + - + +
70A VAL* 3.8 22.7 - - + -
74A PHE* 4.7 3.1 - - + -
75A LYS* 1.3 79.3 - - - +
77A GLU* 1.3 64.0 + - - +
38B VAL* 3.4 27.4 - - + +
39B TYR* 3.9 14.4 - - + -
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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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25A ILE* 4.4 1.3 - - - +
26A LEU 4.0 0.7 - - - +
65A TYR* 3.0 49.1 + - + -
66A ASN 3.5 4.5 - - - -
67A ARG* 4.4 5.6 - - + +
76A VAL* 1.3 75.5 - - - +
78A ASN* 1.3 60.0 - - - +
79A HIS* 3.7 15.4 + - + +
37B LEU 3.9 15.9 - - - +
38B VAL* 2.6 47.6 + - + +
40B LYS* 5.6 6.2 - - - +
46B LYS* 5.6 4.3 + - - -
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Residues in contact with ASN 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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25A ILE* 3.1 7.8 - - + -
26A LEU* 2.7 34.7 + - - +
65A TYR* 4.1 0.4 - - - -
66A ASN* 2.5 47.4 + - + +
68A VAL* 4.2 15.7 - - + +
76A VAL 3.9 0.2 + - - -
77A GLU* 1.3 69.6 - - - +
79A HIS* 1.3 66.2 + - - +
80A THR* 3.5 2.8 + - - +
94A NAG 1.5 61.5 + - - +
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Residues in contact with HIS 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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12A LEU* 3.3 25.8 - - + +
26A LEU* 3.2 23.1 + - - +
27A GLN* 3.2 3.2 - - - -
28A CYS* 2.9 29.4 + - - -
62A ALA* 3.5 22.0 - - + +
64A SER 3.8 3.6 - - - -
65A TYR* 3.9 11.7 - + + -
77A GLU* 4.1 17.6 - - + +
78A ASN* 1.3 74.0 - - - +
80A THR* 1.3 61.0 + - - +
81A ALA 4.8 0.4 - - - +
94A NAG 4.4 3.6 + - - -
36B ASP* 3.1 41.2 + - + -
37B LEU 3.5 14.0 + - - -
38B VAL* 3.7 10.7 - - + +
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Residues in contact with THR 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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12A LEU* 3.4 18.5 - - - +
64A SER* 2.8 30.0 + - - -
65A TYR* 3.5 7.8 - - - -
66A ASN* 3.7 22.7 + - - +
78A ASN 4.3 1.3 - - - +
79A HIS* 1.3 74.6 - - - +
81A ALA* 1.3 61.3 + - - +
94A NAG 3.4 26.6 + - - +
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Residues in contact with ALA 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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12A LEU* 4.7 2.5 - - - -
28A CYS* 3.7 1.3 - - - -
62A ALA* 3.3 7.6 - - - +
63A LYS* 2.5 48.2 + - + -
64A SER* 3.2 20.5 + - - +
79A HIS 3.8 0.8 - - - -
80A THR* 1.3 81.5 - - - +
82A CYS* 1.3 62.1 + - - +
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Residues in contact with CYS 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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10A CYS* 4.0 15.9 - - - +
11A THR* 3.5 27.1 - - + -
12A LEU* 3.6 14.0 - - - +
28A CYS* 2.0 55.0 - - - -
61A VAL 3.4 1.3 - - - -
63A LYS* 4.3 5.6 - - - +
81A ALA* 1.3 75.5 - - - +
83A HIS* 1.3 69.3 + - - +
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Residues in contact with HIS 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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10A CYS* 4.0 7.6 - - - -
59A CYS 3.3 0.5 - - - +
60A CYS* 3.7 0.2 - - - -
61A VAL* 3.0 46.7 + - + +
62A ALA 4.7 0.4 + - - -
63A LYS* 3.1 54.8 + - + +
82A CYS* 1.3 79.5 - - - +
84A CYS* 1.3 61.9 + - - +
85A SER* 3.5 28.1 + - - -
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Residues in contact with CYS 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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10A CYS* 3.7 17.0 - - - +
31A CYS 4.0 2.0 - - - -
32A CYS* 2.0 50.7 - - - -
33A PHE 5.0 0.4 - - - -
58A THR* 3.3 21.4 + - + -
59A CYS 3.1 4.5 - - - -
83A HIS* 1.3 76.4 - - - +
85A SER* 1.3 58.4 + - - +
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Residues in contact with SER 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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58A THR* 3.0 12.4 + - - -
59A CYS 2.4 42.4 + - - -
61A VAL* 4.1 9.6 - - - -
83A HIS* 3.5 31.6 + - - -
84A CYS* 1.3 76.3 - - - +
86A THR* 1.3 68.9 + - - -
96B VAL* 6.2 0.7 - - - -
74C LYS* 3.4 20.3 + - - -
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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