Contacts of the strand formed by residues 158 - 164 (chain O) 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 ASN 158 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156O ASN 3.5 3.4 + - - -
157O LEU* 1.3 70.9 - - - +
159O VAL* 1.3 60.8 + - - +
160O SER* 5.3 0.5 + - - -
201O GLU 3.8 0.9 - - - +
202O ALA* 3.3 18.9 - - - -
203O LYS* 3.4 28.8 + - + +
2101O NAG 1.4 72.1 + - - +
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Residues in contact with VAL 159 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125O PHE* 4.4 3.6 - - + -
157O LEU* 3.1 27.9 + - + -
158O ASN* 1.3 74.7 + - - +
160O SER* 1.3 71.3 + - - +
171O VAL* 5.0 0.9 - - - +
172O PRO* 3.2 28.0 - - - +
179O TRP* 3.5 58.0 - - + +
185O PHE* 3.9 6.4 - - + -
200O CYS* 3.9 17.3 - - + -
201O GLU 3.5 6.5 - - - +
202O ALA* 3.9 8.7 - - + -
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Residues in contact with SER 160 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158O ASN 5.5 0.4 - - - -
159O VAL* 1.3 76.7 - - - +
161O LEU* 1.3 61.4 + - - +
169O ARG* 4.2 13.5 - - - -
170O PHE 3.3 14.4 - - - -
171O VAL* 4.1 16.8 - - - -
185O PHE* 3.8 5.6 - - - -
200O CYS* 3.5 2.6 - - - -
201O GLU* 2.8 54.8 + - - +
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Residues in contact with LEU 161 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148O ILE* 3.2 37.7 - - + -
160O SER* 1.3 72.4 - - - +
162O CYS* 1.3 63.2 + - - +
169O ARG* 3.2 4.9 - - - -
170O PHE* 2.6 45.3 + - + +
185O PHE* 3.5 32.2 - - + -
187O ILE* 3.8 19.1 - - + -
192O ILE* 4.2 15.7 - - + -
198O VAL* 4.2 3.6 - - + -
199O PHE 3.7 28.9 - - - +
200O CYS* 4.1 13.5 - - - -
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Residues in contact with CYS 162 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160O SER 4.0 1.0 + - - -
161O LEU* 1.3 73.2 - - - +
163O ALA* 1.3 65.3 + - - +
164O ARG* 4.1 10.5 - - - -
167O GLU* 3.9 19.1 - - - -
168O LYS 3.5 9.6 - - - -
169O ARG* 3.5 31.6 - - + +
197O MET 4.1 0.2 - - - +
198O VAL* 3.0 6.0 - - - +
199O PHE* 2.8 74.4 + - + +
201O GLU* 5.4 1.3 - - + -
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Residues in contact with ALA 163 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161O LEU* 4.1 0.4 + - + -
162O CYS* 1.3 73.4 - - - +
164O ARG* 1.3 64.5 + - - +
166O PRO 3.3 1.4 - - - +
167O GLU* 3.3 3.6 - - - -
168O LYS 2.9 34.9 + - - +
170O PHE* 4.4 6.3 - - + -
192O ILE* 4.3 14.4 - - + -
194O TYR* 3.5 17.3 - - + +
195O ALA* 3.9 8.7 - - + -
197O MET 3.5 4.7 - - - -
198O VAL* 3.7 19.1 - - + -
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Residues in contact with ARG 164 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123D ASP* 2.8 24.4 + - - -
126D TRP* 5.8 0.2 - - - -
162O CYS* 4.1 5.6 - - - -
163O ALA* 1.3 80.1 - - - +
165O TYR* 1.3 94.8 + - + +
166O PRO 3.5 2.0 - - - -
167O GLU* 3.2 37.3 + - + -
169O ARG* 5.9 0.8 - - - +
195O ALA* 3.5 3.9 - - - +
196O GLY* 2.8 28.2 + - - -
197O MET* 3.0 27.8 + - + +
199O PHE* 3.6 37.1 - - + -
210O GLN* 5.6 0.8 + - - -
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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