Contacts of the strand formed by residues 388 - 392 (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 LEU 388 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309A TRP* 3.6 31.9 - - + -
330A ILE* 4.2 2.9 - - + +
347A PHE* 3.3 18.6 - - + +
348A ILE* 3.7 1.8 - - - -
349A THR* 3.3 38.1 - - - +
381A ALA 4.7 0.7 - - - +
383A THR* 2.7 39.6 + - + +
385A ASP* 2.9 11.6 + - + +
386A SER* 4.1 3.6 - - - +
387A LEU* 1.3 78.7 - - - +
389A ASP* 1.3 62.9 + - - +
390A SER 3.8 7.4 - - - +
391A PHE* 3.5 38.4 - - + -
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Residues in contact with ASP 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A ASN* 2.9 46.8 + - - +
93A PHE* 4.1 4.0 - - + -
261A TYR* 2.6 27.8 + - - +
297A ARG* 2.6 37.4 + - - +
346A PHE* 3.3 19.7 - - - +
347A PHE 2.6 13.4 + - - +
348A ILE* 4.2 0.9 - - + -
381A ALA* 3.3 14.0 - - - +
383A THR* 4.2 0.2 - - - -
386A SER 4.5 1.6 - - - +
387A LEU 3.6 1.0 + - - -
388A LEU* 1.3 73.7 - - - +
390A SER* 1.3 62.9 + - - +
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Residues in contact with SER 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A PHE* 3.5 41.3 - - - -
347A PHE 3.8 1.2 + - - -
348A ILE* 3.3 24.1 - - - +
349A THR 3.4 4.2 + - - -
379A PRO* 5.3 0.3 - - - +
380A SER* 3.3 19.4 + - - -
381A ALA 4.0 0.2 + - - -
383A THR* 3.7 7.2 - - - -
388A LEU* 3.2 5.2 - - - +
389A ASP* 1.3 83.6 - - - +
391A PHE* 1.3 83.7 + - - +
392A VAL* 3.8 0.9 - - - +
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Residues in contact with PHE 391 (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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309A TRP* 3.4 38.1 - + - -
349A THR* 3.7 5.6 - - - +
351A GLN* 4.3 13.9 - - + -
377A ILE* 3.4 31.6 - - + +
378A ARG 3.7 17.7 - - - +
379A PRO* 3.3 14.0 - - + +
380A SER* 3.0 24.4 + - - +
382A ASN 4.1 4.9 - - - -
383A THR* 3.7 24.9 - - + -
388A LEU* 3.5 18.2 - - + -
390A SER* 1.3 89.2 + - - +
392A VAL* 1.3 59.6 + - - +
502A NAG 3.5 28.9 - - - -
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Residues in contact with VAL 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A PHE* 3.8 34.1 - - + -
133A PHE* 4.0 17.7 - - + -
165A GLN* 4.6 2.7 - - - +
348A ILE* 4.0 13.0 - - + -
349A THR* 3.0 31.0 + - - +
350A ASP* 3.2 3.3 - - - -
351A GLN 2.8 26.5 + - - +
379A PRO* 4.3 8.1 - - + -
390A SER* 3.8 4.7 - - - +
391A PHE* 1.3 83.3 - - - +
393A TRP* 1.3 67.6 + - - +
394A VAL* 3.7 17.7 - - + -
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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