Contacts of the strand formed by residues 200 - 204 (chain A) in PDB entry 1QO0
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 200 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135A LEU* 5.2 10.1 - - + -
139A TYR* 3.2 44.4 - - + -
140A GLY 4.5 6.5 - - - +
142A ARG 3.0 7.0 + - - +
143A VAL* 3.2 27.3 - - + +
144A VAL 3.1 23.4 + - - -
164A TYR* 3.7 17.0 - - + +
198A ALA* 3.3 4.3 - - - +
199A ASP* 1.3 84.5 - - - +
201A VAL* 1.3 65.1 + - - +
202A PHE* 5.6 0.4 - - + -
227A PRO* 4.2 1.1 - - - -
228A PRO* 3.6 11.7 - - + +
230A ALA* 5.7 3.1 - - + +
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Residues in contact with VAL 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A VAL* 3.6 26.2 - - + +
146A ILE* 4.0 25.8 - - + -
193A ILE* 3.8 19.3 - - + -
198A ALA* 5.1 0.7 - - + -
200A VAL* 1.3 74.6 - - - +
202A PHE* 1.3 61.3 + - - +
217A ILE* 4.7 9.9 - - + -
227A PRO* 4.4 17.5 - - + +
228A PRO 3.0 7.7 + - - +
229A ILE* 3.9 29.6 - - + -
230A ALA* 2.7 34.4 + - - +
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Residues in contact with PHE 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A LEU* 3.9 23.3 - - + -
135A LEU* 4.5 16.6 - - + -
143A VAL* 3.9 10.8 - - + -
144A VAL 2.9 9.5 + - - -
145A PHE* 3.5 27.8 - + + -
146A ILE 3.1 24.1 + - - +
156A SER* 4.7 2.7 - - - -
157A ASN* 3.2 27.0 - - - +
160A MET* 3.6 33.2 - - + -
164A TYR* 5.8 0.2 - - + -
200A VAL* 3.9 1.7 + - + -
201A VAL* 1.3 73.8 - - - +
203A SER* 1.3 58.2 + - - +
204A THR* 3.8 18.6 + - + -
230A ALA* 3.3 13.7 - - - +
232A LEU* 3.9 24.7 - - + -
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Residues in contact with SER 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A ILE* 3.2 17.1 + - - +
201A VAL* 3.7 0.9 + - - -
202A PHE* 1.3 73.8 - - - +
204A THR* 1.3 62.2 + - - +
205A VAL* 3.3 23.4 + - - +
210A THR* 5.5 0.2 - - - +
213A LEU* 4.3 1.7 - - - +
214A TYR* 4.3 11.0 - - - -
229A ILE* 3.8 24.0 - - - -
230A ALA 2.7 11.4 + - - -
231A SER* 2.7 36.3 + - - -
232A LEU 3.5 4.7 + - - -
234A THR* 4.8 0.5 + - - -
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Residues in contact with THR 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A ILE 2.8 7.5 + - - -
147A GLY* 3.2 19.7 - - - -
148A SER 3.4 2.4 + - - -
153A PRO* 3.3 38.0 - - + +
156A SER* 4.0 19.1 - - - +
157A ASN* 3.5 14.0 + - - +
202A PHE* 3.8 28.9 + - + -
203A SER* 1.3 76.4 - - - +
205A VAL* 1.3 63.7 + - - +
206A VAL* 3.5 4.9 - - - +
232A LEU* 4.5 8.7 - - + -
233A THR* 3.3 12.6 - - + -
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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