Contacts of the strand formed by residues 156 - 163 (chain D) in PDB entry 2X1W
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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125C GLU* 3.7 5.5 - - - +
129C THR* 3.8 20.5 + - + +
165C CYS* 2.0 50.5 - - + -
138D ILE 3.0 20.9 - - - +
139D ASP* 3.6 19.1 - - - -
140D VAL* 4.1 1.3 - - - -
154D PRO* 3.6 18.1 - - - +
155D PRO* 1.3 89.5 - - - +
157D VAL* 1.3 66.7 + - - +
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Residues in contact with VAL 157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125C GLU* 3.4 9.9 - - + +
129C THR* 3.6 4.9 - - - -
136D VAL 3.7 0.3 - - - +
137D ALA* 3.6 3.5 - - - -
138D ILE* 3.0 38.0 + - + +
140D VAL* 4.0 7.0 - - + -
156D CYS* 1.3 78.3 - - - +
158D SER* 1.3 58.9 + - - +
159D VAL* 4.0 7.7 + - + -
183D LYS* 3.5 26.2 - - + -
185D LEU* 3.6 26.7 - - + -
203D PHE* 3.7 41.3 - - + -
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Residues in contact with SER 158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125C GLU* 2.7 13.9 + - - -
128C LYS* 3.7 36.7 + - - +
129C THR* 3.8 4.6 - - - +
135D GLU* 3.4 30.3 + - - +
136D VAL 3.5 6.8 + - - -
157D VAL* 1.3 70.7 - - - +
159D VAL* 1.3 73.0 + - - +
181D LEU* 4.9 0.9 - - - +
183D LYS* 3.2 16.6 + - - -
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Residues in contact with VAL 159 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135D GLU* 3.5 1.3 - - - -
136D VAL* 2.9 27.6 + - - +
138D ILE* 3.6 31.9 - - + -
157D VAL* 4.5 4.0 - - + -
158D SER* 1.3 86.9 + - - +
160D TYR* 1.3 67.8 + - - +
161D ARG* 3.9 11.9 - - + +
181D LEU* 4.3 11.2 - - + -
183D LYS* 3.7 16.8 - - - -
203D PHE* 4.1 15.7 - - + -
204D ALA 3.7 23.1 - - - +
205D ASN* 3.9 6.1 - - - +
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Residues in contact with TYR 160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133D PRO* 3.8 14.8 - - + -
134D ARG* 3.2 7.2 - - - -
135D GLU* 3.3 50.1 + - + +
158D SER* 5.9 0.2 - - - -
159D VAL* 1.3 77.8 - - - +
161D ARG* 1.3 68.8 + - - +
205D ASN* 2.8 22.6 + - - +
206D HIS* 2.9 30.1 + - - +
1P NAG 3.4 47.2 + - - +
2P NAG 3.3 29.2 + - - -
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Residues in contact with ARG 161 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133D PRO* 4.2 2.2 - - - -
134D ARG* 2.8 32.3 + - - +
136D VAL* 3.8 26.7 - - + +
138D ILE* 3.6 14.8 - - + +
143D GLU* 2.8 39.4 + - - -
159D VAL* 3.9 14.1 - - + +
160D TYR* 1.3 76.9 + - - +
162D CYS* 1.3 67.9 - - - +
163D GLY* 3.4 1.2 + - - -
203D PHE* 4.3 4.2 - - - +
204D ALA* 2.9 48.3 + - - +
206D HIS* 3.4 25.8 - - + +
1K NAG 5.0 4.7 + - - -
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Residues in contact with CYS 162 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132D MET 3.6 0.9 - - - -
161D ARG* 1.3 74.5 - - - +
163D GLY* 1.3 58.2 + - - +
173D CYS* 3.9 26.0 - - - +
174D MET* 4.1 4.0 - - - -
175D ASN* 3.4 31.9 - - - +
206D HIS* 2.9 19.5 + - + +
208D SER 3.7 1.8 - - - -
209D CYS* 2.0 48.5 - - - -
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Residues in contact with GLY 163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131D CYS* 3.4 1.0 - - - -
132D MET 3.1 25.4 + - - -
134D ARG* 3.0 26.2 + - - -
161D ARG 3.4 2.0 + - - -
162D CYS* 1.3 75.8 - - - +
164D GLY* 1.3 60.2 + - - -
173D CYS* 3.6 10.0 - - - -
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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