Contacts of the strand formed by residues 197 - 203 (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 MET 197 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123D ASP* 2.8 51.6 - - - +
126D TRP* 3.9 21.1 - - + -
164O ARG* 3.0 40.5 + - + +
165O TYR* 3.7 17.9 - - + -
195O ALA* 3.5 1.1 - - - +
196O GLY* 1.3 80.5 - - - +
198O VAL* 1.3 67.6 + - - +
199O PHE* 5.7 3.4 - - + -
213O MET* 3.3 39.3 - - + +
214O TYR 3.2 14.6 - - - +
215O ILE* 4.6 0.7 - - - -
216O VAL* 3.8 2.0 - - - -
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Residues in contact with VAL 198 (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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136O VAL* 4.9 3.1 - - + -
148O ILE* 3.7 28.3 - - + -
161O LEU* 4.2 7.2 - - + -
162O CYS 3.0 9.0 - - - +
163O ALA* 3.7 20.6 - - + -
192O ILE* 3.9 21.1 - - + -
195O ALA* 4.4 0.9 - - + -
197O MET* 1.3 81.0 - - - +
199O PHE* 1.3 66.6 + - - +
213O MET* 4.1 1.2 - - - +
214O TYR* 3.0 47.8 + - + +
216O VAL* 3.8 18.8 - - + -
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Residues in contact with PHE 199 (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* 3.8 6.1 - - - -
162O CYS* 2.8 63.7 + - + +
164O ARG* 3.6 43.3 - - - -
169O ARG* 4.9 1.6 - - - -
197O MET* 5.6 3.4 - - + -
198O VAL* 1.3 81.5 - - - +
200O CYS* 1.3 71.0 + - - +
201O GLU* 4.2 13.9 - - + -
210O GLN* 3.4 35.4 - - + -
211O SER* 3.6 17.0 - - - +
212O ILE 3.7 9.2 - - - +
213O MET* 4.5 11.2 - - + -
214O TYR* 4.7 2.7 - - - -
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Residues in contact with CYS 200 (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* 3.7 13.9 - - + -
148O ILE* 4.3 8.7 - - - -
150O CYS* 2.0 56.5 - - + -
159O VAL* 3.9 6.5 - - + -
160O SER 3.5 5.4 - - - -
161O LEU* 4.1 8.7 - - - -
185O PHE* 4.0 14.8 - - - -
199O PHE* 1.3 77.6 - - - +
201O GLU* 1.3 62.2 + - - +
210O GLN* 3.4 3.8 - - - -
211O SER* 2.9 30.7 + - - +
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Residues in contact with GLU 201 (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* 4.3 0.9 - - - -
158O ASN 3.8 1.0 - - - +
159O VAL* 3.5 1.6 - - - +
160O SER* 2.8 48.3 + - - +
162O CYS* 5.4 0.4 - - + -
169O ARG* 2.7 42.0 + - - +
199O PHE* 4.2 17.6 - - + +
200O CYS* 1.3 79.2 - - - +
202O ALA* 1.3 65.5 + - - +
203O LYS 4.3 0.3 + - - -
208O SER* 4.6 18.7 - - - -
209O TYR 3.4 14.4 - - - +
210O GLN* 4.7 6.1 - - + +
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Residues in contact with ALA 202 (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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124O PRO* 5.7 1.6 - - + -
125O PHE* 4.0 9.0 - - + -
157O LEU* 3.8 38.6 - - + -
158O ASN 3.3 12.1 - - - +
159O VAL* 3.9 8.5 - - + -
201O GLU* 1.3 77.6 - - - +
203O LYS* 1.3 60.3 + - - +
204O ILE* 6.1 0.4 - - + -
207O GLU 3.9 0.5 - - - +
208O SER* 3.8 2.3 - - - -
209O TYR* 3.1 36.9 + - + +
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Residues in contact with LYS 203 (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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157O LEU* 4.8 1.4 - - - +
158O ASN* 3.4 40.8 + - + +
201O GLU 4.3 0.4 + - - -
202O ALA* 1.3 76.7 - - - +
204O ILE* 1.3 66.1 + - - +
205O ASN* 3.6 16.3 + - - +
207O GLU 3.6 8.1 - - - +
208O SER* 4.8 5.2 - - - +
209O TYR* 5.8 0.2 - - - -
2101O NAG 3.3 43.4 + - + +
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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