Contacts of the strand formed by residues 156 - 163 (chain E) in PDB entry 2X1X
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 CYS 156 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137E ALA* 4.4 15.3 - - + -
138E ILE 3.3 24.2 - - - +
139E ASP* 3.7 15.5 - - - -
140E VAL* 3.9 2.2 - - - -
154E PRO* 3.2 18.8 - - - +
155E PRO* 1.3 93.5 - - + +
157E VAL* 1.3 71.0 + - - +
185E LEU* 4.2 0.9 - - - +
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Residues in contact with VAL 157 (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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136E VAL 3.6 0.7 - - - +
137E ALA* 3.6 5.4 - - - -
138E ILE* 3.0 39.0 + - + +
140E VAL* 3.9 1.8 - - + -
156E CYS* 1.3 80.6 - - - +
158E SER* 1.3 60.0 + - - +
159E VAL* 3.6 9.0 + - + -
183E LYS* 3.7 26.9 - - + -
185E LEU* 3.8 24.2 - - + -
203E PHE* 3.8 42.8 - - + -
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Residues in contact with SER 158 (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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135E GLU* 3.1 33.5 + - - +
136E VAL 3.7 6.3 - - - -
137E ALA* 4.9 0.9 - - - +
157E VAL* 1.3 70.9 - - - +
159E VAL* 1.3 66.9 + - - +
160E TYR* 5.3 2.1 - - - -
181E LEU* 5.8 0.3 - - - +
183E LYS* 3.6 18.6 + - - +
205E ASN* 5.5 0.2 - - - +
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Residues in contact with VAL 159 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135E GLU* 4.4 0.2 - - - -
136E VAL* 2.9 33.7 + - - +
138E ILE* 3.6 35.4 - - + -
157E VAL* 4.3 6.5 - - + +
158E SER* 1.3 80.3 + - - +
160E TYR* 1.3 65.6 + - - +
161E ARG* 4.0 17.9 - - + +
181E LEU* 4.9 4.7 - - + -
183E LYS* 3.8 18.6 - - - -
203E PHE* 4.2 18.8 - - + +
204E ALA 4.2 9.9 - - - +
205E ASN* 4.4 10.5 - - - +
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Residues in contact with TYR 160 (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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1B NAG 4.0 23.6 - - - -
2B NAG 3.4 27.1 + - - -
133E PRO* 3.9 15.3 - - + -
134E ARG* 3.4 12.3 - - - -
135E GLU* 3.4 50.6 + - + +
158E SER* 5.3 1.6 - - - -
159E VAL* 1.3 78.4 - - - +
161E ARG* 1.3 63.8 + - - +
205E ASN* 3.2 26.9 + - - +
206E HIS* 2.9 36.7 + - - +
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Residues in contact with ARG 161 (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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1A NAG 4.8 6.9 + - - -
133E PRO* 4.2 2.2 - - - -
134E ARG* 2.6 39.8 + - - +
136E VAL* 3.7 26.8 - - + +
138E ILE* 3.9 15.7 - - + +
143E GLU* 3.4 36.5 + - - -
159E VAL* 3.7 14.1 + - + +
160E TYR* 1.3 76.4 + - - +
162E CYS* 1.3 64.5 + - - +
163E GLY 3.4 0.9 + - - -
203E PHE* 4.5 5.9 - - - +
204E ALA* 2.9 47.6 + - - +
206E HIS* 3.4 24.4 - - + +
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Residues in contact with CYS 162 (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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132E MET 3.6 4.7 - - - -
161E ARG* 1.3 74.0 - - - +
163E GLY* 1.3 58.9 + - - +
173E CYS* 3.9 18.3 - - - +
174E MET* 4.4 0.9 - - - -
175E ASN* 3.4 36.8 - - - +
206E HIS* 3.2 18.7 + - + +
209E CYS* 2.0 50.0 - - + -
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Residues in contact with GLY 163 (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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130E GLN 3.4 0.3 - - - +
131E CYS* 3.2 0.2 - - - -
132E MET 3.0 30.6 + - - -
134E ARG* 3.3 17.6 - - - +
161E ARG 3.4 3.0 + - - -
162E CYS* 1.3 74.5 - - - +
164E GLY* 1.3 62.0 + - - -
173E CYS* 3.1 12.7 - - - -
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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