Contacts of the strand formed by residues 346 - 350 (chain A) in PDB entry 1QK0
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 PHE 346 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261A TYR* 4.1 2.8 - - - -
297A ARG* 2.9 46.1 + - - -
298A GLY* 3.1 4.1 - - - -
299A LEU 2.9 24.4 + - - -
344A ASN* 3.2 37.5 - - + -
345A ALA* 1.3 76.3 - - - +
347A PHE* 1.3 68.7 + - - +
386A SER* 3.2 33.2 - - - -
387A LEU* 3.6 12.3 - - + +
389A ASP* 3.3 27.1 - - - +
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Residues in contact with PHE 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A TYR* 4.1 2.0 - - - -
299A LEU* 3.1 39.0 - - + +
301A THR* 4.4 7.9 - - + -
329A TYR* 6.1 0.2 - + - -
330A ILE* 3.5 51.8 - - + -
333A ILE* 3.8 20.4 - - + -
334A GLY* 3.8 18.4 - - - -
337A LEU* 4.0 10.1 - - + -
345A ALA 3.8 15.7 - - - -
346A PHE* 1.3 76.5 - - - +
348A ILE* 1.3 69.1 + - - +
387A LEU* 2.8 32.6 + - + +
388A LEU* 3.3 9.0 - - + -
389A ASP* 2.6 32.2 + - - +
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Residues in contact with ILE 348 (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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93A PHE* 3.4 36.1 - - + -
133A PHE* 4.7 5.4 - - + -
217A VAL* 4.1 15.7 - - + -
261A TYR* 3.5 41.3 - - + +
299A LEU 3.1 1.4 + - - +
300A ALA* 3.3 20.3 - - + -
301A THR 3.0 23.2 + - - -
347A PHE* 1.3 78.8 - - - +
349A THR* 1.3 65.0 + - - +
388A LEU* 3.7 0.7 - - - -
389A ASP* 4.2 0.4 - - + -
390A SER 3.3 18.2 - - - +
392A VAL* 4.0 15.7 - - + -
394A VAL* 5.4 0.4 - - + -
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Residues in contact with THR 349 (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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301A THR* 3.0 29.8 + - - +
302A ASN* 3.8 0.4 - - + -
309A TRP* 4.6 6.5 - - + -
326A GLU* 3.6 30.2 - - + +
330A ILE* 4.5 7.3 - - - +
348A ILE* 1.3 76.6 + - - +
350A ASP* 1.3 73.9 + - - +
351A GLN* 3.6 11.9 + - + +
388A LEU* 3.3 20.6 - - - +
390A SER 3.4 5.5 + - - -
391A PHE* 3.7 5.1 - - - -
392A VAL* 3.0 25.8 + - - -
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Residues in contact with ASP 350 (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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301A THR 3.0 8.6 + - - +
302A ASN* 2.7 52.5 + - - +
303A VAL* 3.9 3.6 - - - -
304A ALA* 3.1 17.6 + - - -
305A ASN 5.3 3.1 - - - -
349A THR* 1.3 71.7 - - - +
351A GLN* 1.3 73.2 + - - +
352A GLY* 3.0 15.3 + - - -
353A ARG 5.6 0.9 - - - -
392A VAL* 3.2 8.4 - - - +
393A TRP* 3.5 0.5 - - - -
394A VAL* 3.2 29.2 + - + +
395A LYS* 3.0 25.9 + - - +
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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