Contacts of the strand formed by residues 447 - 452 (chain A) in PDB entry 3Q8A
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 GLN 447 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331A THR* 3.3 27.6 - - + +
332A VAL 3.3 18.2 - - - +
333A ALA* 5.1 1.1 - - + -
334A ILE* 3.8 7.9 - - - +
385A LEU* 4.3 7.8 - - - +
386A GLY 4.9 3.6 + - - -
442A LEU* 4.3 1.9 - - - +
445A THR* 3.1 25.8 + - - +
446A LYS* 1.3 79.8 - - - +
448A LEU* 1.3 73.5 + - - +
449A ARG* 5.4 3.2 - - - +
601A ASN* 5.7 1.8 + - - -
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Residues in contact with LEU 448 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A MET* 5.0 7.2 - - + -
269A ILE* 4.2 13.9 - - + -
331A THR* 3.7 0.3 - - - -
332A VAL* 2.9 41.7 + - + +
334A ILE* 4.6 8.5 - - + +
360A LEU* 3.9 24.5 - - + -
383A LEU* 3.5 24.7 - - + -
384A VAL 3.4 16.2 - - - +
385A LEU* 3.5 26.2 - - + +
391A LEU* 3.6 16.2 - - + -
442A LEU* 4.4 11.4 - - + -
447A GLN* 1.3 83.2 - - - +
449A ARG* 1.3 59.7 + - - +
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Residues in contact with ARG 449 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A THR* 5.9 0.2 - - - -
329A SER* 3.1 28.5 - - - +
330A SER 3.5 7.4 - - - +
331A THR* 4.2 12.6 - - + +
382A SER 3.5 0.3 - - - +
383A LEU* 3.4 9.7 - - - +
384A VAL* 3.1 57.7 + - - +
385A LEU* 5.3 0.2 - - - +
386A GLY 3.7 9.7 + - - -
387A LYS* 3.4 22.9 + - - +
388A ASN* 5.0 0.6 - - - +
447A GLN* 5.4 3.3 - - - +
448A LEU* 1.3 74.3 - - - +
450A LEU* 1.3 60.6 + - - +
451A ASP* 2.8 31.6 + - - +
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Residues in contact with LEU 450 (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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263A HIS* 5.7 0.9 - - - +
264A VAL* 3.2 41.0 + - + +
266A MET* 4.3 17.0 - - + +
295A THR* 4.4 0.4 - - + -
328A ASN 3.5 1.6 - - - +
329A SER* 3.5 4.6 - - - -
330A SER* 2.9 34.0 + - - +
332A VAL* 3.6 27.6 - - + -
364A ILE* 5.8 0.7 - - + -
381A THR* 3.7 21.8 - - + -
382A SER 3.5 3.8 - - - +
383A LEU* 4.2 17.3 - - + -
394A ILE* 4.0 17.3 - - + -
449A ARG* 1.3 78.2 - - - +
451A ASP* 1.3 65.4 + - - +
452A THR* 3.7 3.8 + - - -
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Residues in contact with ASP 451 (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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327A SER* 6.2 3.1 - - - -
328A ASN 3.4 5.8 - - - +
329A SER* 2.8 24.0 + - - -
380A THR 4.0 0.9 - - - +
381A THR* 3.2 4.9 - - - +
382A SER* 3.0 35.5 + - - +
384A VAL* 3.4 13.1 - - - +
449A ARG* 2.8 37.4 + - - -
450A LEU* 1.3 71.2 - - - +
452A THR* 1.3 60.0 + - - +
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Residues in contact with THR 452 (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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262A VAL* 4.4 11.4 - - + +
263A HIS* 5.0 2.9 - - - -
264A VAL* 3.9 10.3 + - + +
327A SER* 5.1 1.0 - - - -
328A ASN* 2.8 42.5 + - + +
379A PRO* 3.3 31.0 - - + -
380A THR 3.7 3.1 - - - -
381A THR* 2.6 26.9 + - - +
450A LEU 4.4 2.9 + - - -
451A ASP* 1.3 73.7 + - - +
453A ASP* 1.3 80.8 + - - +
454A GLN* 4.5 0.9 - - - +
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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