Contacts of the strand formed by residues 290 - 296 (chain A) in PDB entry 1QFM
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 TYR 290 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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250A SER* 4.4 3.3 + - - -
259A ASN* 2.9 37.4 + - - +
261A LEU* 4.1 14.4 - - + +
283A ILE* 3.6 33.3 - - + +
285A ASN* 5.4 1.0 + - - -
287A GLU* 5.9 0.3 - - - +
288A GLY* 3.5 26.9 + - - -
289A GLU* 1.3 73.1 - - - +
291A ASP* 1.3 65.7 + - - +
292A TYR 4.0 1.7 + - - -
302A PHE* 3.9 18.8 - - + -
303A LYS 3.5 2.7 - - - -
304A THR* 3.4 22.0 - - - -
306A ARG* 3.5 31.4 + - + +
314A ILE* 4.1 10.1 - - + -
316A ILE* 4.4 9.4 - - + -
326A TRP* 3.5 32.8 - + - -
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Residues in contact with ASP 291 (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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252A ARG* 3.8 7.3 + - - -
289A GLU* 2.6 36.8 - - - +
290A TYR* 1.3 74.4 - - - +
292A TYR* 1.3 66.2 + - - +
293A VAL* 3.4 2.7 + - + +
302A PHE* 3.2 5.2 - - - -
303A LYS* 2.8 72.3 + - + +
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Residues in contact with TYR 292 (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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239A GLU* 3.5 32.8 + - - +
240A LEU 4.3 2.5 - - - -
241A SER* 3.7 15.9 - - - -
242A ASP* 2.8 33.8 + - - -
248A LEU* 3.4 26.7 - - + -
261A LEU* 5.9 1.3 - - + +
290A TYR 4.0 1.4 + - - -
291A ASP* 1.3 73.0 - - - +
293A VAL* 1.3 63.9 + - - +
294A THR* 3.3 30.1 - - - -
295A ASN* 2.6 27.1 + - - -
300A PHE* 3.5 26.2 - + - -
301A THR 4.2 2.0 - - - -
302A PHE* 3.6 14.2 - + + -
341A VAL 5.3 1.0 - - - +
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Residues in contact with VAL 293 (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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242A ASP* 3.7 8.1 - - - +
291A ASP* 3.8 10.8 - - + +
292A TYR* 1.3 82.4 - - - +
294A THR* 1.3 67.3 + - - +
301A THR* 2.9 21.1 + - + +
303A LYS* 3.9 7.2 - - + +
313A LEU* 3.9 25.1 - - + -
341A VAL* 3.8 32.8 - - + +
342A ALA* 5.5 0.2 - - - -
343A CYS* 3.9 15.1 + - + +
349A LEU* 3.7 29.6 - - + -
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Residues in contact with THR 294 (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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242A ASP* 2.8 17.9 + - - -
292A TYR* 3.3 20.6 - - - -
293A VAL* 1.3 86.0 - - + +
295A ASN* 1.3 68.9 + - - +
296A GLU* 5.5 0.2 - - + -
301A THR* 2.8 31.6 + - - +
343A CYS* 3.6 23.6 - - + -
366A LEU* 3.8 30.5 - - + -
389A LYS* 3.0 19.7 + - - +
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Residues in contact with ASN 295 (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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241A SER* 3.4 10.6 - - - -
242A ASP* 3.8 4.2 + - - +
243A ASP* 2.9 29.1 + - - +
246A TYR* 4.4 2.2 - - - -
292A TYR* 2.6 23.7 + - - -
294A THR* 1.3 86.9 + - - +
296A GLU* 1.3 73.3 + - - +
297A GLY 2.9 22.4 + - - +
299A VAL 3.2 13.7 - - - +
300A PHE* 3.6 33.4 - - + -
301A THR* 5.3 0.2 - - - -
389A LYS* 4.0 5.9 + - - -
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Residues in contact with GLU 296 (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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294A THR* 5.5 0.4 - - + -
295A ASN* 1.3 77.0 - - - +
297A GLY* 1.3 64.2 + - - +
298A THR 3.3 0.5 + - - -
299A VAL* 2.9 30.8 + - + +
346A SER* 4.0 3.3 - - - +
347A ASN* 6.0 0.2 - - - +
366A LEU* 3.9 22.6 - - + +
389A LYS* 2.8 32.0 + - - -
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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