Contacts of the strand formed by residues 70 - 78 (chain A) in PDB entry 5TE0
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 LYS 70 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49A ASP* 5.8 2.7 - - - +
62A LEU* 4.1 19.3 - - + -
63A VAL 3.4 6.5 - - - +
64A ARG* 4.8 3.1 - - + +
68A GLY 3.5 8.1 + - - +
69A MET* 1.3 80.8 - - - +
71A CYS* 1.3 62.8 + - - +
127A ASP* 5.5 0.3 - - - -
128A PHE* 3.7 43.1 + - + +
130A ARG* 6.5 0.2 - - - -
401A XIN 6.4 0.4 - - - -
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Residues in contact with CYS 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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62A LEU* 3.6 5.6 - - - +
63A VAL* 2.8 37.6 + - + +
65A THR* 3.7 29.4 - - - -
69A MET* 3.7 11.0 - - - -
70A LYS* 1.3 79.1 - - - +
72A ALA* 1.3 58.8 + - - +
107A ILE* 3.5 23.6 - - - -
125A LEU* 3.7 22.0 - - + -
126A MET 3.5 11.7 - - - +
128A PHE* 3.9 9.6 - - - +
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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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52A LEU* 4.6 5.2 - - + -
60A VAL* 4.4 5.4 - - + -
61A PHE 3.2 7.9 - - - +
71A CYS* 1.3 72.1 - - - +
73A LEU* 1.3 58.0 + - - +
125A LEU* 3.6 5.4 - - - +
126A MET* 2.9 51.1 + - + +
127A ASP 4.0 0.9 - - - +
128A PHE* 4.1 2.5 - - - +
401A XIN 3.5 41.3 - - + +
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Residues in contact with LEU 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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39A PHE* 3.9 32.1 - - + -
41A ILE* 4.0 22.7 - - + -
46A VAL* 4.0 11.4 - - + -
48A VAL* 4.7 0.2 - - + -
59A ILE 3.6 1.9 - - - +
60A VAL* 3.3 3.4 - - - -
61A PHE* 2.7 50.3 + - + +
63A VAL* 3.6 32.1 - - + -
71A CYS 4.1 0.2 + - - -
72A ALA* 1.3 72.8 - - - +
74A LYS* 1.3 71.0 + - - +
75A ARG* 4.7 0.9 - - + +
123A LEU* 4.1 9.6 - - + -
124A ILE 3.5 20.9 - - - +
125A LEU* 4.1 2.9 - - + -
126A MET* 3.9 1.8 - - - -
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Residues in contact with LYS 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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58A ALA* 4.4 10.3 - - + -
59A ILE 3.4 8.5 - - - +
60A VAL* 4.3 15.9 - - + +
73A LEU* 1.3 73.8 - - - +
75A ARG* 1.3 60.8 + - - +
76A MET* 4.1 33.2 - - + -
90A GLU* 3.5 25.6 + - - +
122A VAL 3.7 1.6 - - - +
123A LEU* 3.4 4.5 - - - -
124A ILE* 2.8 48.6 + - + +
126A MET* 3.5 18.3 - - + +
194A ASP* 3.7 24.7 + - - -
196A GLY* 5.1 2.6 - - - -
401A XIN 4.4 12.9 + - - +
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Residues in contact with ARG 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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34A TYR* 3.2 36.9 + - - -
37A ARG* 4.3 7.7 - - - +
39A PHE* 3.3 30.4 - - - -
57A PHE 3.9 0.9 - - - +
58A ALA* 3.4 2.9 - - - -
59A ILE* 2.8 38.5 + - + +
61A PHE* 4.2 19.5 - - + -
73A LEU* 3.9 1.7 + - + -
74A LYS* 1.3 73.7 - - - +
76A MET* 1.4 64.6 + - - +
77A PHE* 3.5 35.8 - - + -
121A GLU* 2.8 34.8 + - + +
122A VAL 3.5 3.6 - - - +
123A LEU* 3.5 20.0 - - + -
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Residues in contact with MET 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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56A GLY 4.3 17.9 - - - +
57A PHE* 3.5 12.6 - - + +
58A ALA* 3.7 19.3 - - + -
74A LYS* 4.1 27.6 - - + -
75A ARG* 1.4 73.2 - - - +
77A PHE* 1.3 75.1 + - - +
78A VAL* 4.1 10.0 + - + -
87A CYS* 4.2 16.8 - - - -
90A GLU* 5.6 2.2 - - - +
120A TRP 3.8 0.3 - - - +
121A GLU* 3.6 3.5 - - - +
122A VAL* 2.7 53.9 + - + +
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Residues in contact with PHE 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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34A TYR* 5.0 4.0 - - - -
57A PHE* 3.4 30.7 + - + +
75A ARG* 3.5 46.9 - - + -
76A MET* 1.3 77.0 - - - +
78A VAL* 1.3 63.4 + - - +
79A ASN* 6.0 0.3 - - - -
114A VAL* 4.6 13.5 - - + -
119A VAL* 4.2 15.9 - - + -
120A TRP 3.5 11.4 - - - -
121A GLU* 3.7 21.8 - - + -
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Residues in contact with VAL 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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76A MET* 4.1 11.9 + - + -
77A PHE* 1.3 78.2 - - - +
79A ASN* 1.4 63.3 + - - +
80A ASN 3.4 10.3 - - - +
83A ASP* 3.6 15.9 - - + +
84A LEU* 3.3 36.1 - - + +
87A CYS* 3.6 30.5 - - - -
119A VAL* 3.4 4.8 - - - +
120A TRP* 2.7 47.2 + - + +
122A VAL* 4.3 9.6 - - + -
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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