Contacts of the strand formed by residues 72 - 79 (chain A) in PDB entry 5TX4
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 ILE 72 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A PHE* 3.5 9.5 - - - +
36A SER* 3.0 42.8 + - - +
37A THR 5.4 1.6 - - - -
38A CYS 3.7 4.7 - - - +
39A ASP* 3.3 43.5 - - + +
65A TRP* 3.5 32.5 - - + +
66A ARG 3.3 4.7 - - - +
67A LYS* 3.9 21.5 - - + -
71A ASN* 1.3 78.3 - - - +
73A THR* 1.3 65.4 + - - +
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Residues in contact with THR 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A VAL* 3.8 26.8 - - + +
34A ARG 3.1 10.1 - - - +
35A PHE* 4.0 16.2 - - + -
36A SER* 4.2 4.0 - - - +
64A VAL 3.7 0.7 + - - +
65A TRP* 3.4 6.9 - - - -
66A ARG* 2.9 53.4 + - - +
71A ASN* 3.8 17.1 + - - +
72A ILE* 1.3 79.1 - - - +
74A LEU* 1.3 60.9 + - - +
75A GLU* 4.2 0.9 - - - -
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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
----------------------------------------------------------
32A ASP 3.4 2.6 - - - +
33A VAL* 4.6 0.7 - - - -
34A ARG* 2.8 37.6 + - + +
36A SER* 4.0 21.0 - - - +
38A CYS* 6.2 2.2 - - + -
44A CYS* 6.3 1.1 - - + -
45A MET 4.8 2.0 - - - +
46A SER* 3.6 44.2 - - - +
48A CYS* 6.2 0.2 - - + -
63A ALA* 4.2 16.8 - - + -
64A VAL 3.2 22.7 - - - +
65A TRP* 4.3 17.0 - - + -
73A THR* 1.3 73.7 - - - +
75A GLU* 1.3 61.4 + - - +
76A THR* 4.1 8.7 + - + +
100A MET* 5.1 0.2 - - + -
124A ILE* 4.2 17.9 - - + -
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Residues in contact with GLU 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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32A ASP* 3.2 22.4 - - - +
33A VAL* 3.9 21.7 - - + +
62A VAL 3.7 0.3 - - - +
63A ALA* 3.1 6.9 - - - +
64A VAL* 2.7 47.3 + - + +
66A ARG* 5.4 3.4 + - - -
73A THR* 4.2 0.6 - - - -
74A LEU* 1.3 72.8 - - - +
76A THR* 1.3 61.9 + - - +
77A VAL* 3.9 11.4 - - + +
85A TYR* 2.6 33.2 + - - -
86A HIS* 2.8 30.4 + - - -
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Residues in contact with THR 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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29A LYS* 3.4 22.9 - - + -
30A PHE* 3.3 1.6 - - - -
31A CYS* 3.0 35.7 + - - +
32A ASP 3.0 27.4 + - - -
46A SER* 4.3 13.5 - - - -
48A CYS* 3.8 4.8 - - + +
62A VAL 3.4 4.5 - - - +
63A ALA* 4.4 3.8 - - + -
74A LEU* 4.3 11.1 + - + +
75A GLU* 1.3 76.6 - - - +
77A VAL* 1.3 64.7 + - - +
121A ASN* 3.6 27.1 - - - +
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Residues in contact with VAL 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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28A CYS* 4.3 0.4 - - - +
29A LYS 3.5 7.5 + - - -
30A PHE* 3.7 15.0 - - + -
32A ASP* 3.6 21.3 - - - +
61A CYS* 3.7 3.1 - - - -
62A VAL* 2.9 51.8 + - + +
64A VAL* 6.3 0.2 - - + -
75A GLU* 3.9 12.8 - - + +
76A THR* 1.3 80.2 - - - +
78A CYS* 1.3 73.5 - - - +
79A HIS* 4.2 3.8 - - + -
85A TYR* 3.7 36.8 - - + +
121A ASN* 3.7 2.8 + - - -
74B ARG* 4.5 2.0 - - - +
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Residues in contact with CYS 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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28A CYS* 3.7 12.6 - - - -
30A PHE* 3.6 34.8 - - + -
52A SER* 4.6 3.1 - - - -
54A CYS* 2.1 58.3 - - + -
59A GLU* 3.9 13.8 - - - +
60A VAL 3.4 5.6 - - - -
77A VAL* 1.3 79.9 - - - +
79A HIS* 1.3 65.4 + - - +
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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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59A GLU* 3.6 9.7 - - - +
60A VAL* 2.9 33.0 + - - +
62A VAL* 3.8 17.0 - - + -
77A VAL* 4.2 7.0 - - + -
78A CYS* 1.3 78.5 + - - +
80A ASP* 1.3 79.1 + - - +
81A PRO* 3.4 2.8 - - - +
83A LEU* 2.9 38.9 + - + -
84A PRO 3.2 19.3 + - - -
85A TYR* 3.5 26.8 - + + -
90A LEU* 3.4 25.8 - - + -
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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