Contacts of the strand formed by residues 51 - 62 (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 THR 51 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43E ARG* 4.1 6.4 + - - +
44E PRO* 3.2 49.6 - - + +
45E ASP* 4.7 8.1 - - + +
50E PRO* 1.3 78.1 - - - +
52E LEU* 1.3 59.7 + - - +
53E ILE* 3.4 20.6 + - - +
82E TRP* 5.3 4.0 - - - -
83E TYR 5.0 6.5 - - - +
107E TRP* 4.6 6.3 - - + -
178E GLU 3.9 11.3 + - - -
179E ILE* 3.8 4.5 - - - +
180E VAL* 3.4 22.7 + - - +
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Residues in contact with LEU 52 (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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50E PRO 3.8 3.8 + - - +
51E THR* 1.3 73.2 - - - +
53E ILE* 1.3 61.5 + - - +
54E HIS* 3.6 24.3 + - + +
81E THR 3.9 3.8 - - - +
82E TRP* 4.3 8.1 - - - +
83E TYR 4.9 2.7 + - - +
180E VAL* 3.5 37.9 - - + +
182E GLN* 3.4 32.1 - - + +
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Residues in contact with ILE 53 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51E THR* 3.4 27.8 - - - +
52E LEU* 1.3 71.5 - - - +
54E HIS* 1.3 73.3 + - - +
55E THR* 4.0 0.6 + - - +
80E GLN* 3.9 19.3 - - + +
81E THR 3.2 6.7 - - - +
82E TRP* 3.5 26.2 - - + -
107E TRP* 4.8 6.7 - - + -
109E PRO* 4.8 5.8 - - + -
179E ILE* 3.5 28.7 - - + -
180E VAL 3.1 7.4 + - - +
181E TYR* 3.4 32.5 - - + -
182E GLN* 3.3 22.5 + - - +
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Residues in contact with HIS 54 (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* 4.0 23.1 + - + +
53E ILE* 1.3 72.6 - - - +
55E THR* 1.3 59.6 + - - +
80E GLN* 3.2 6.8 - - - +
81E THR* 2.8 48.2 + - + +
82E TRP* 5.8 0.9 - - - -
83E TYR* 6.4 1.8 - + - -
182E GLN* 3.3 42.4 + - - +
183E TRP 4.5 5.2 + - - -
184E LYS* 4.4 25.3 - - + +
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Residues in contact with THR 55 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53E ILE* 4.0 3.6 + - - +
54E HIS* 1.3 77.5 + - - +
56E ASP* 1.3 68.8 + - - +
57E MET* 5.2 0.9 - - + +
78E PHE* 3.7 24.9 - - + -
79E ALA 3.6 4.5 - - - +
80E GLN* 4.4 2.1 - - + +
169E PHE* 3.6 29.1 - - + -
181E TYR* 3.4 28.9 - - - +
182E GLN 3.0 11.0 + - - -
183E TRP* 3.5 26.0 - - + -
184E LYS* 3.7 14.8 + - - +
223E MET* 5.6 0.7 - - - -
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Residues in contact with ASP 56 (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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206D SER* 5.9 0.5 - - - -
410D FYP 3.9 21.5 - - - +
55E THR* 1.3 78.4 - - - +
57E MET* 1.3 69.3 + - - +
77E PHE 4.2 0.2 - - - +
79E ALA* 2.8 42.0 + - + +
183E TRP* 4.5 0.9 - - - -
184E LYS* 3.8 31.6 + - + +
187E SER* 2.8 32.0 + - - +
188E VAL* 4.6 0.2 - - - -
189E GLU* 5.7 2.9 - - - +
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Residues in contact with MET 57 (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 4.9 1.5 - - - +
55E THR* 5.7 0.2 - - + -
56E ASP* 1.3 80.9 + - - +
58E TYR* 1.3 61.9 + - - +
59E VAL* 4.7 11.9 - - + -
76E ILE* 3.8 34.5 - - + -
77E PHE 4.0 4.9 - - - +
78E PHE* 4.4 22.7 - - + +
113E PHE* 5.8 0.9 - - + -
167E LEU* 4.6 14.1 - - + -
169E PHE* 3.6 34.1 - - + -
183E TRP* 4.1 13.0 - - + -
187E SER 3.1 17.8 + - - +
188E VAL* 3.6 20.1 - - + -
189E GLU* 3.7 2.3 + - - +
225E VAL* 4.9 13.0 - - + -
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Residues in contact with TYR 58 (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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205D SER* 4.8 3.4 - - - -
206D SER* 5.3 0.4 - - - -
410D FYP 3.4 52.7 + - + -
57E MET* 1.3 75.0 - - - +
59E VAL* 1.3 78.6 + - - +
60E ASN* 3.5 16.8 + - + -
76E ILE* 3.6 1.5 - - - -
77E PHE* 3.0 42.2 + + + +
189E GLU* 3.3 38.6 - - + +
190E VAL 5.1 3.8 - - - -
191E GLY* 4.4 17.4 - - - -
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Residues in contact with VAL 59 (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* 4.7 13.2 - - + -
58E TYR* 1.3 81.1 - - - +
60E ASN* 1.3 64.7 + - - +
61E SER 4.1 9.0 - - - +
62E ILE* 4.2 23.6 - - + -
74E ILE* 4.4 18.6 - - + -
75E ASP 4.1 2.2 - - - -
76E ILE* 4.1 16.6 - - + -
188E VAL* 5.2 6.7 - - + -
189E GLU 3.4 16.9 + - - +
190E VAL* 4.1 20.0 - - + -
191E GLY 4.1 3.8 + - - -
196E TRP* 4.5 12.1 - - + -
227E PHE* 5.3 7.4 - - + -
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Residues in contact with ASN 60 (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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102D HIS 3.9 20.0 + - - -
58E TYR* 3.5 11.7 + - + -
59E VAL* 1.3 75.4 - - - +
61E SER* 1.3 63.4 + - - +
75E ASP* 2.8 26.6 + - - +
77E PHE* 3.7 31.5 - - + -
144E ARG* 4.2 9.7 - - - +
191E GLY 4.0 6.1 - - - +
192E ASP* 5.6 1.0 - - - +
196E TRP* 3.5 14.4 + - - -
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Residues in contact with SER 61 (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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138D GLU* 4.5 16.0 + - - -
59E VAL* 3.8 1.1 - - - -
60E ASN* 1.3 85.0 - - - +
62E ILE* 1.3 68.9 + - - +
63E GLY* 4.1 1.4 + - - -
74E ILE* 3.7 2.8 - - - +
75E ASP* 3.0 41.5 + - - +
195E SER 5.0 6.1 - - - -
196E TRP* 4.0 17.0 - - - +
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Residues in contact with ILE 62 (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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59E VAL* 4.2 13.7 - - + -
61E SER* 1.3 80.1 - - - +
63E GLY* 1.3 72.1 + - - +
65E VAL* 4.7 7.6 - - + -
72E TYR* 4.4 15.9 - - + -
73E THR 3.4 10.1 - - - +
74E ILE* 4.4 4.9 - - + +
196E TRP* 2.7 71.5 - - + +
197E ARG* 4.7 0.3 - - - +
198E LEU* 4.7 13.1 - - + +
203E PHE* 4.4 2.9 - - + -
227E PHE* 3.6 36.6 - - + -
229E LEU* 5.6 2.7 - - + -
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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