Contacts of the strand formed by residues 159 - 164 (chain N) 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 VAL 159 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125N PHE* 4.2 4.7 - - + -
157N LEU* 3.4 13.7 + - + +
158N ASN* 1.3 76.6 - - - +
160N SER* 1.3 71.5 + - - +
172N PRO* 3.3 28.3 - - - +
179N TRP* 3.3 61.6 - - + +
185N PHE* 3.5 10.3 - - + -
200N CYS* 3.8 22.4 - - + -
201N GLU 3.4 8.3 - - - +
202N ALA* 4.3 4.7 - - + -
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Residues in contact with SER 160 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269L HIS* 4.2 14.7 + - - -
158N ASN 4.1 0.6 + - - -
159N VAL* 1.3 75.4 - - - +
161N LEU* 1.3 59.8 + - - +
162N CYS* 4.4 0.2 - - - -
169N ARG* 2.7 46.6 + - - +
170N PHE 3.7 7.6 - - - -
171N VAL* 4.6 4.0 - - - -
172N PRO* 4.9 0.4 - - - -
185N PHE* 4.0 3.4 - - - -
200N CYS* 3.5 3.6 - - - -
201N GLU* 2.7 42.0 + - - +
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Residues in contact with LEU 161 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148N ILE* 3.8 31.0 - - + -
160N SER* 1.3 73.3 - - - +
162N CYS* 1.3 66.3 + - - +
168N LYS 3.7 0.5 - - - +
169N ARG* 3.4 2.3 - - - -
170N PHE* 2.8 43.5 + - + +
185N PHE* 3.7 30.7 - - + -
187N ILE* 4.0 20.0 - - + -
192N ILE* 4.2 12.3 - - + -
198N VAL* 4.3 9.2 - - + -
199N PHE* 3.2 32.8 - - - +
200N CYS* 4.0 13.5 - - - +
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Residues in contact with CYS 162 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160N SER* 4.4 0.2 - - - -
161N LEU* 1.3 74.8 - - - +
163N ALA* 1.3 60.8 + - - +
164N ARG* 5.6 1.8 - - - +
167N GLU* 6.5 1.6 - - + -
168N LYS 3.2 8.1 - - - +
169N ARG* 3.5 42.2 - - - -
198N VAL* 3.2 6.2 - - - +
199N PHE* 3.0 72.4 + - + -
201N GLU* 3.9 10.8 - - - -
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Residues in contact with ALA 163 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161N LEU* 4.0 0.6 + - + -
162N CYS* 1.3 74.9 - - - +
164N ARG* 1.3 64.1 + - - +
166N PRO 3.1 0.9 - - - +
167N GLU* 3.2 5.0 - - - +
168N LYS 2.8 32.1 + - - +
170N PHE* 4.4 16.6 - - + -
192N ILE* 4.6 3.4 - - + -
194N TYR* 3.3 20.9 - - + +
195N ALA* 3.8 7.6 - - + -
197N MET 3.5 5.6 - - - -
198N VAL* 3.7 19.5 - - + -
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Residues in contact with ARG 164 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A ASP* 3.4 30.1 + - - -
126A TRP* 5.5 0.2 - - - -
162N CYS* 5.6 2.2 - - - +
163N ALA* 1.3 77.8 - - - +
165N TYR* 1.3 91.4 + - + +
166N PRO 3.2 3.1 - - - -
167N GLU* 3.5 29.7 + - + +
195N ALA* 3.9 4.1 - - - +
196N GLY* 2.9 25.9 + - - -
197N MET* 3.2 39.2 + - + +
199N PHE* 3.9 32.3 - - + -
213N MET* 4.7 7.1 - - - +
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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