Contacts of the strand formed by residues 298 - 304 (chain A) in PDB entry 1QCO
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 298 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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296A ASP* 4.4 8.3 + - - -
297A ILE* 1.3 70.0 - - - +
299A LEU* 1.3 61.7 + - - +
300A SER* 5.7 0.2 - - - -
317A SER 3.8 6.7 - - - +
318A ASN* 3.4 16.9 + - - +
394A GLY* 3.0 5.7 - - - -
395A HIS* 2.9 48.9 + - + +
397A GLN* 5.0 12.9 - - - +
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Residues in contact with LEU 299 (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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200A LEU* 4.0 31.0 - - + -
202A MET* 4.1 10.3 - - + -
230A LEU* 3.8 29.6 - - + -
297A ILE* 3.8 17.0 - - + +
298A ASN* 1.3 80.3 - - - +
300A SER* 1.3 62.5 + - - +
316A ARG* 3.4 5.4 - - - +
317A SER 3.0 34.0 + - - +
318A ASN* 4.3 2.9 - - - -
319A PHE 4.0 15.9 - - - +
351A ILE* 3.5 33.2 - - + -
393A THR 3.4 2.5 - - - +
394A GLY* 4.0 6.3 - - - -
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Residues in contact with SER 300 (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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299A LEU* 1.3 77.1 - - - +
301A VAL* 1.3 66.1 + - - +
302A SER* 5.8 0.7 - - - -
313A THR* 3.6 22.3 + - - +
315A CYS 3.5 4.8 + - - -
316A ARG* 4.4 8.0 + - - +
391A ILE 3.7 1.0 - - - +
392A ILE* 3.3 5.4 - - - +
393A THR* 2.9 46.8 + - - -
395A HIS* 6.0 2.0 - - - -
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Residues in contact with VAL 301 (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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198A MET* 3.4 30.5 - - + -
200A LEU* 4.1 27.8 - - + -
300A SER* 1.3 78.5 + - - +
302A SER* 1.3 56.1 + - - +
313A THR* 3.4 5.2 - - - +
314A ILE* 2.8 37.0 + - + -
315A CYS* 2.9 33.0 + - + -
390A VAL* 3.7 20.9 - - + -
391A ILE 3.5 3.6 - - - +
392A ILE* 4.0 16.6 - - + -
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Residues in contact with SER 302 (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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300A SER* 4.3 0.6 - - - -
301A VAL* 1.3 77.9 - - - +
303A LEU* 1.3 60.9 + - - +
311A ALA* 4.2 16.3 - - - +
312A ALA 3.1 17.0 - - - -
313A THR* 4.2 7.9 - - - -
314A ILE* 4.9 0.2 - - - -
389A GLU 3.7 0.7 - - - +
390A VAL* 3.4 7.1 - - - +
391A ILE* 2.9 52.3 + - - +
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Residues in contact with LEU 303 (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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302A SER* 1.3 75.6 - - - +
304A LYS* 1.3 64.6 + - - +
305A GLY 4.0 12.6 - - - +
308A MET* 4.1 7.8 - - - +
311A ALA* 3.4 1.7 - - - -
312A ALA* 2.8 33.4 + - - +
314A ILE* 4.3 22.4 - - + +
362A MET* 3.8 22.0 - - + -
375A VAL* 4.4 14.6 - - + -
381A ARG* 4.3 13.5 - - + +
384A LEU* 3.7 29.6 - - + -
388A ASP* 4.0 18.8 - - + +
389A GLU 3.3 9.6 - - - +
390A VAL* 4.8 4.3 - - + -
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Residues in contact with LYS 304 (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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303A LEU* 1.3 78.5 - - - +
305A GLY* 1.3 67.9 + - - +
308A MET* 3.2 26.7 - - + +
309A SER* 3.6 19.0 + - - +
310A GLN* 4.2 3.8 - - - +
311A ALA* 3.6 27.8 - - + +
387A GLY 3.9 2.1 - - - +
388A ASP* 3.6 0.5 - - - -
389A GLU* 2.9 45.2 + - + +
391A ILE* 6.4 2.0 - - + -
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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