Contacts of the strand formed by residues 284 - 290 (chain A) in PDB entry 3QWR
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 ILE 284 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219A LEU* 4.1 1.1 - - - +
221A LEU* 3.6 22.4 - - + -
230A VAL* 4.9 0.7 - - + -
232A VAL* 3.9 19.7 - - + -
253A VAL* 3.8 26.5 - - + -
254A GLN 3.5 4.7 - - - +
255A VAL* 3.6 18.6 - - + -
276A VAL* 3.7 18.2 - - + -
278A CYS* 3.2 28.5 - - - -
283A SER* 1.3 72.4 - - - +
285A SER* 1.3 64.0 + - - +
286A VAL* 4.7 0.9 - - + -
301A ALA 3.9 0.3 - - - +
302A SER* 3.0 1.7 + - - -
303A VAL* 2.8 45.1 + - + +
305A CYS* 3.8 8.3 - - - -
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Residues in contact with SER 285 (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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253A VAL* 3.3 4.5 - - - +
254A GLN* 2.7 49.7 + - - -
256A GLN* 5.3 3.5 + - - +
283A SER 4.0 2.6 + - - -
284A ILE* 1.3 69.0 - - - +
286A VAL* 1.3 64.1 + - - +
300A TRP* 3.3 30.3 - - - +
301A ALA 3.1 7.9 - - - -
302A SER* 2.8 23.9 + - - -
5D PRO* 4.7 12.0 - - - +
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Residues in contact with VAL 286 (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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216A PRO* 3.4 25.1 - - + +
219A LEU* 3.9 20.6 - - + -
232A VAL* 4.4 1.6 - - + -
234A TRP* 3.8 48.0 - - + -
251A PHE* 4.2 3.8 - - + -
252A CYS 3.2 10.1 - - - +
253A VAL* 4.0 17.0 - - + -
284A ILE* 4.7 1.1 - - + -
285A SER* 1.3 80.3 - - - +
287A ARG* 1.3 68.0 + - - +
300A TRP* 3.7 2.7 - - - -
301A ALA* 2.9 31.4 + - + +
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Residues in contact with ARG 287 (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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216A PRO* 4.1 4.7 - - - -
251A PHE* 3.2 8.8 - - - +
252A CYS* 3.0 40.1 + - + +
266A ARG* 3.7 11.1 - - - +
268A PHE* 5.7 1.8 - - - -
286A VAL* 1.3 73.5 - - - +
288A ALA* 1.3 60.9 + - - +
297A TRP* 3.6 40.6 - - + +
298A SER* 3.5 29.1 + - - +
299A GLU 3.9 4.0 - - - +
300A TRP* 3.5 40.6 - - + +
7D ASP* 3.6 20.8 + - - -
25D ASP* 3.0 42.2 + - - +
26D TYR* 5.6 0.8 + - - -
88D ILE* 4.6 8.1 - - - +
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Residues in contact with ALA 288 (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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213A PRO* 3.9 8.6 - - + +
214A ASP 4.7 2.2 - - - +
216A PRO* 4.4 7.4 - - + +
237A PRO* 5.5 1.1 - - + -
249A LEU* 4.2 16.2 - - + -
250A THR 3.3 5.8 - - - +
251A PHE* 3.6 26.0 - - + -
287A ARG* 1.3 73.5 - - - +
289A GLN* 1.3 61.1 + - - +
297A TRP* 3.4 5.1 - - - -
298A SER* 2.7 46.1 + - - +
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Residues in contact with GLN 289 (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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213A PRO* 4.2 4.9 - - - -
249A LEU* 3.3 9.8 - - - +
250A THR* 2.9 35.4 + - - +
288A ALA* 1.3 75.7 - - - +
290A ASP* 1.3 69.4 + - - +
294A SER* 3.4 28.3 + - - +
295A SER 2.8 24.2 + - - +
296A SER 4.2 4.7 - - - +
297A TRP* 3.3 38.7 + - + +
25D ASP 5.2 0.6 + - - -
26D TYR* 3.8 18.4 - - - -
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Residues in contact with ASP 290 (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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114A TYR* 2.5 37.3 + - - +
213A PRO* 4.5 4.8 - - - +
240A TRP* 3.5 11.9 - - + -
247A PHE 5.7 0.2 - - - -
248A SER 4.2 4.8 - - - +
249A LEU* 3.9 11.6 - - - +
250A THR* 4.8 0.9 + - - -
289A GLN* 1.3 88.0 - - - +
291A ARG* 1.3 64.5 + - - +
292A TYR* 3.0 26.5 + - - +
293A TYR* 3.1 10.0 + - - +
294A SER* 3.3 26.1 + - - +
295A SER* 3.9 7.5 + - - +
159B ARG* 3.2 17.9 + - - -
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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