Contacts of the strand formed by residues 72 - 82 (chain E) in PDB entry 6D6U
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 TYR 72 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62E ILE* 4.4 9.4 - - + -
64E PRO 3.9 6.3 - - - -
65E VAL* 3.5 26.7 - - + -
71E GLU* 1.3 80.6 + - - +
73E THR* 1.3 72.2 + - - +
74E ILE* 4.2 21.0 - - + +
147E ILE 3.8 0.2 - - - +
148E ASP* 2.8 18.4 - - - +
149E ALA* 3.1 47.4 + - + +
151E CYS* 3.7 19.7 - - + -
165E CYS* 3.5 27.9 + - + -
166E PRO 3.0 24.4 + - - -
167E LEU* 4.2 9.2 - - - +
227E PHE* 4.5 17.6 - + - -
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Residues in contact with THR 73 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62E ILE* 3.3 9.4 - - - +
63E GLY* 2.4 43.3 + - - +
64E PRO* 3.9 16.2 + - + +
71E GLU* 4.3 6.1 + - - -
72E TYR* 1.3 77.4 + - - +
74E ILE* 1.3 69.7 + - - +
75E ASP* 6.0 0.7 - - + -
146E THR* 4.4 13.9 - - + -
147E ILE 3.4 7.6 + - - +
148E ASP* 4.7 6.2 - - + +
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Residues in contact with ILE 74 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57E MET* 6.0 0.4 - - - -
59E VAL* 4.4 14.4 - - + -
61E SER 3.7 10.8 - - - +
62E ILE* 4.4 4.0 - - + -
63E GLY 5.3 0.2 - - - -
72E TYR* 4.2 15.0 + - + -
73E THR* 1.3 77.4 - - - +
75E ASP* 1.3 68.1 + - - +
76E ILE* 3.7 22.0 - - + -
146E THR* 3.5 9.0 - - - +
147E ILE* 2.9 62.8 + - + +
149E ALA* 6.1 0.7 - - + -
167E LEU* 4.3 18.6 - - + -
227E PHE* 4.0 31.4 - - + -
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Residues in contact with ASP 75 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105D LYS* 5.9 3.6 - - - +
59E VAL* 4.1 0.2 - - - -
60E ASN* 2.8 38.8 + - - +
61E SER* 3.0 28.4 + - - +
73E THR* 6.0 0.7 - - + -
74E ILE* 1.3 77.9 - - - +
76E ILE* 1.3 64.2 + - - +
77E PHE* 5.1 0.3 - - - -
122E HIS* 4.6 2.4 + - - -
144E ARG* 3.5 31.3 + - - -
145E LEU 2.8 22.1 - - - +
146E THR* 3.7 11.6 + - + +
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Residues in contact with ILE 76 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57E MET* 3.8 30.5 - - + -
58E TYR 3.5 8.7 - - - +
59E VAL* 4.1 13.9 - - + -
74E ILE* 3.7 32.8 - - + -
75E ASP* 1.3 81.0 + - - +
77E PHE* 1.3 71.8 + - - +
78E PHE* 4.3 10.1 - - + +
113E PHE* 4.2 18.6 - - + -
144E ARG* 4.0 1.4 - - - +
145E LEU* 3.3 34.2 + - + +
147E ILE* 3.8 23.8 - - + +
167E LEU* 4.7 4.5 - - + -
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Residues in contact with PHE 77 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100D PHE* 4.6 15.3 - + - -
102D HIS* 5.8 2.9 - + - -
160D TYR* 4.3 17.7 - + - -
410D FYP 3.8 72.1 - + - +
56E ASP 4.2 0.2 - - - +
57E MET* 4.0 1.6 - - - -
58E TYR* 3.0 45.1 + + + +
60E ASN* 3.7 33.0 - - + -
75E ASP* 5.1 0.4 - - - -
76E ILE* 1.3 81.6 - - - +
78E PHE* 1.3 66.0 + - - +
79E ALA* 3.5 2.4 + - - +
142E THR* 4.4 1.3 - - - +
143E LEU 3.8 6.5 - - - -
144E ARG* 4.5 23.6 - - + +
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Residues in contact with PHE 78 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A THR* 5.2 5.6 - - + -
55E THR* 3.7 29.2 - - + -
57E MET* 4.4 19.3 - - + -
76E ILE* 3.9 6.2 - - + +
77E PHE* 1.3 71.2 - - - +
79E ALA* 1.3 54.8 + - - +
80E GLN* 3.2 43.1 - - + -
111E THR* 4.0 21.8 - - + -
113E PHE* 4.3 13.7 - + - -
142E THR* 2.8 22.5 + - - -
143E LEU* 3.0 43.4 + - + +
145E LEU* 3.9 20.6 - - + +
169E PHE* 4.1 20.9 - + - -
181E TYR* 5.5 0.2 - + - -
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Residues in contact with ALA 79 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410D FYP 3.4 28.3 - - - +
55E THR* 3.7 1.7 - - - +
56E ASP* 2.8 50.7 + - + +
77E PHE 4.1 0.9 - - - +
78E PHE* 1.3 79.7 - - - +
80E GLN* 1.3 59.2 - - - +
81E THR* 5.4 0.2 - - - -
140E LEU* 5.0 8.5 - - + -
141E TYR 3.6 5.8 - - - +
142E THR* 3.5 6.7 - - - +
184E LYS* 5.8 2.7 + - - +
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Residues in contact with GLN 80 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A THR* 5.9 3.2 - - - +
53E ILE* 3.9 16.4 - - + +
54E HIS 3.2 11.9 - - - +
55E THR* 4.4 4.3 - - - +
78E PHE* 3.2 35.6 - - + -
79E ALA* 1.3 74.4 - - - +
81E THR* 1.3 65.5 + - - +
82E TRP* 3.5 14.7 - - + -
109E PRO* 3.5 32.2 + - - +
111E THR* 3.7 13.8 + - - -
140E LEU* 3.8 1.6 - - - +
141E TYR* 3.0 50.4 + - + +
143E LEU* 5.4 0.2 - - - +
181E TYR* 4.1 3.8 - - - -
184E LYS* 6.4 0.4 - - - +
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Residues in contact with THR 81 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52E LEU 3.9 0.5 - - - +
53E ILE* 3.2 4.7 - - - -
54E HIS* 2.8 49.9 + - + +
80E GLN* 1.3 72.7 - - - +
82E TRP* 1.3 68.1 + - - +
83E TYR* 5.7 1.1 - - + -
134E TRP* 5.5 0.7 - - + -
138E ARG* 4.0 34.3 + - + +
139E VAL 3.2 15.7 - - - +
140E LEU* 3.1 25.4 - - + +
184E LYS* 4.1 14.8 + - - -
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Residues in contact with TRP 82 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44E PRO* 4.7 2.7 - - + -
51E THR* 5.3 4.3 - - - -
52E LEU 4.3 7.2 - - - +
53E ILE* 3.5 26.2 - - + -
54E HIS* 5.8 0.9 - - - -
80E GLN* 3.5 22.9 - - + -
81E THR* 1.3 87.3 - - - +
83E TYR* 1.3 82.2 + - - +
84E ASP* 4.4 9.1 + - + +
106E ILE* 5.3 0.4 - - + -
107E TRP* 3.6 47.9 + + - +
108E ILE* 4.7 1.8 - - + -
109E PRO* 3.4 32.3 - - + -
131E LEU* 5.7 0.4 - - + -
138E ARG* 4.2 0.9 - - - -
139E VAL* 3.1 51.7 + - + +
141E TYR* 3.6 26.9 - + + -
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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