Contacts of the strand formed by residues 161 - 166 (chain E) in PDB entry 1I3R
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 161 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91E VAL* 6.4 0.2 - - - -
105E LEU* 3.7 23.6 - - + -
121E TRP* 4.9 4.5 - - + -
122E LEU 3.1 11.0 - - - +
123E ARG* 3.4 35.9 + - + -
151E LEU* 3.5 28.7 - - + -
153E PHE* 3.5 36.6 - + + +
154E LEU 4.0 3.5 + - - -
159E ASP* 3.1 39.2 + - + -
160E PHE* 1.3 76.6 - - - +
162E ASP* 1.3 64.4 + - - +
177E HIS* 3.0 8.1 + - - -
178E TRP* 2.7 57.0 + + + +
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Residues in contact with ASP 162 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91E VAL* 6.5 0.2 - - - -
120E THR 3.7 0.3 - - - +
121E TRP* 3.6 5.9 - - - -
122E LEU* 2.7 53.0 + - + +
125E GLY* 4.8 3.3 + - - -
160E PHE* 4.0 17.5 - - - -
161E TYR* 1.3 76.9 - - - +
163E CYS* 1.3 60.3 + - - +
164E GLU 3.8 0.2 - - - -
175E ARG* 3.4 39.5 + - + +
176E LYS 3.1 4.6 - - - +
177E HIS* 2.8 38.0 + - - +
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Residues in contact with CYS 163 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89E VAL* 4.8 1.4 - - - +
91E VAL* 3.5 18.5 - - + +
107E CYS* 2.0 51.4 - - + -
119E VAL* 3.9 21.3 - - - -
120E THR 3.8 2.9 - - - -
121E TRP* 4.0 13.6 - - + -
162E ASP* 1.3 72.1 - - - +
164E GLU* 1.3 60.8 + - - +
165E VAL* 3.8 7.0 + - - +
174E LEU 3.6 1.4 - - - +
175E ARG* 3.4 2.1 - - - -
176E LYS* 2.8 31.1 + - + +
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Residues in contact with GLU 164 (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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118E ASN 3.5 1.6 - - - +
119E VAL* 3.2 4.0 - - - -
120E THR* 2.7 64.4 + - - +
122E LEU* 4.2 11.6 - - + +
162E ASP 3.8 0.6 + - - -
163E CYS* 1.3 71.8 - - - +
165E VAL* 1.3 62.7 + - - +
166E ASP* 5.3 1.3 - - + +
173E PRO* 4.0 26.2 - - + +
174E LEU 3.3 10.3 - - - +
175E ARG* 3.2 36.1 + - + +
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Residues in contact with VAL 165 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87E PRO* 4.2 24.9 - - + -
89E VAL* 3.8 24.0 - - + -
109E ILE* 3.7 35.0 - - + -
117E VAL* 4.6 8.1 - - + -
118E ASN 3.3 6.1 - - - +
119E VAL* 4.3 2.9 - - + -
163E CYS* 3.9 17.7 - - - +
164E GLU* 1.3 75.4 - - - +
166E ASP* 1.3 68.2 + - - +
170E LEU* 3.4 7.7 - - + +
173E PRO* 4.6 0.9 - - - -
174E LEU* 2.7 36.3 + - + +
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Residues in contact with ASP 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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117E VAL* 3.6 5.0 - - - +
118E ASN* 2.7 48.3 + - + +
164E GLU* 4.2 1.5 + - + -
165E VAL* 1.3 74.4 - - - +
167E HIS* 1.3 71.0 + - - +
170E LEU* 4.4 5.3 - - - +
172E GLU 4.8 0.2 - - - -
173E PRO* 3.7 35.0 - - + +
1K NAG 3.5 31.3 + - - +
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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