Contacts of the strand formed by residues 162 - 167 (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 GLU 162 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154E GLN* 4.1 16.3 + - - +
157E ASN* 4.7 5.5 + - - +
160E MET 3.5 11.6 + - - +
161E ASP* 1.3 79.8 - - - +
163E HIS* 1.3 65.8 + - - +
164E SER* 3.7 3.1 + - - -
228E ASP* 5.3 12.3 - - + +
229E LEU 3.3 10.3 - - - +
230E SER* 5.1 6.5 - - - -
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Residues in contact with HIS 163 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151E CYS* 4.9 5.8 - - - -
152E GLN 4.4 1.8 - - - +
153E LEU* 3.4 30.3 - - + +
154E GLN* 2.4 51.7 + - + +
155E LEU* 3.4 22.3 - - + +
161E ASP* 4.0 20.1 + - + +
162E GLU* 1.3 75.0 - - - +
164E SER* 1.3 58.2 + - - +
165E CYS* 4.2 2.0 + - - -
201E PHE* 3.9 28.3 - + + -
228E ASP* 3.4 3.3 - - - +
229E LEU* 2.7 49.2 + - + +
231E ARG* 4.2 1.6 + - - +
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Residues in contact with SER 164 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151E CYS* 3.4 11.0 - - - -
152E GLN* 4.1 12.5 + - - +
154E GLN* 6.0 0.2 - - - +
162E GLU 3.7 2.8 + - - -
163E HIS* 1.3 74.2 - - - +
165E CYS* 1.3 59.2 + - - +
166E PRO* 3.5 9.0 - - - +
207E ARG* 5.6 0.7 - - - -
226E TYR* 4.4 18.1 - - - -
227E PHE 4.0 1.6 - - - -
228E ASP* 3.1 22.2 - - - -
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Residues in contact with CYS 165 (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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65E VAL* 5.5 4.3 - - - -
72E TYR* 3.5 33.6 + - + -
151E CYS* 2.0 42.4 - - - -
153E LEU* 5.1 2.0 - - - -
163E HIS* 5.1 2.7 - - - -
164E SER* 1.3 73.0 - - - +
166E PRO* 1.3 66.0 - - - +
201E PHE* 6.3 0.7 - - - -
226E TYR* 3.5 16.3 - - - +
227E PHE* 3.4 27.4 + - + +
229E LEU* 4.2 22.2 - - - +
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Residues in contact with PRO 166 (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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72E TYR* 3.0 14.7 + - + -
115E ASN* 3.1 31.2 - - - +
149E ALA* 3.9 4.7 - - - +
150E GLU 3.8 14.8 - - - +
151E CYS* 4.2 4.0 - - - -
152E GLN* 4.5 5.2 - - + +
164E SER* 3.5 9.9 - - - +
165E CYS* 1.3 87.0 - - + +
167E LEU* 1.3 60.3 + - - +
168E GLU* 5.3 8.7 - - - +
224E SER* 5.4 3.4 - - - +
226E TYR* 3.4 18.6 - - + -
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Residues in contact with LEU 167 (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* 4.6 22.9 - - + -
72E TYR* 4.2 6.3 - - - +
74E ILE* 4.3 28.9 - - + -
76E ILE* 4.7 9.9 - - + -
113E PHE* 4.3 20.9 - - + -
115E ASN* 4.7 4.5 - - + -
147E ILE* 4.1 25.4 - - + -
149E ALA* 4.5 9.9 - - + -
165E CYS 5.2 0.4 - - - +
166E PRO* 1.3 77.3 - - - +
168E GLU* 1.3 62.2 + - - +
169E PHE* 4.3 8.5 + - + -
224E SER* 3.7 0.8 + - - -
225E VAL* 2.9 43.3 + - + +
227E PHE* 5.8 3.6 - - + -
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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