Contacts of the strand formed by residues 409 - 416 (chain A) in PDB entry 3KQ4
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 HIS 409 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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315A ILE* 3.3 47.0 - - + +
317A THR* 2.5 30.4 + - + -
331A GLU* 4.7 3.1 - - + +
390A SER 3.7 0.5 - - - -
391A GLY* 2.7 47.3 + - - +
407A HIS 3.9 1.4 + - - +
408A GLU* 1.3 75.0 - - - +
410A ILE* 1.3 59.2 + - - +
411A THR* 3.6 13.9 + - - -
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Residues in contact with ILE 410 (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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314A VAL* 4.8 9.9 - - + -
315A ILE 2.8 11.1 + - - +
316A TYR* 3.3 27.8 - - + -
317A THR 2.8 24.4 + - - -
343A LEU* 3.9 35.7 - - + -
388A PHE* 4.2 6.3 - - + -
389A LEU 3.7 12.1 - - - +
390A SER* 3.7 13.2 - - - +
395A LEU* 4.1 10.1 - - + -
402A TYR* 4.5 4.7 - - + -
404A PRO* 5.0 1.6 - - + -
408A GLU* 3.5 38.1 + - + +
409A HIS* 1.3 72.5 - - - +
411A THR* 1.3 66.8 + - - +
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Residues in contact with THR 411 (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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317A THR* 3.5 23.8 - - + +
319A ASN* 4.7 10.5 - - + +
388A PHE* 3.6 2.6 - - - -
389A LEU* 3.0 45.0 + - + +
391A GLY 3.8 14.7 + - - -
409A HIS* 3.6 22.7 + - - -
410A ILE* 1.3 80.1 - - - +
412A ALA* 1.3 70.7 + - - +
413A ASN* 4.0 4.5 - - + +
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Residues in contact with ALA 412 (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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316A TYR* 3.8 13.5 - - + +
317A THR 3.0 13.1 + - - +
318A ILE* 4.5 1.3 - - + -
319A ASN 3.0 17.2 + - - -
373A ILE* 4.1 12.6 - - + -
386A TRP* 3.0 17.2 - - + -
387A GLN 3.4 5.8 - - - +
388A PHE* 3.4 33.4 - - + -
411A THR* 1.3 75.2 - - - +
413A ASN* 1.3 58.5 + - - +
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Residues in contact with ASN 413 (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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319A ASN* 3.4 28.6 + - - +
321A GLN* 4.2 14.9 - - - +
386A TRP* 3.3 4.9 - - - -
387A GLN* 2.7 53.9 + - - +
389A LEU* 4.3 14.9 - - + +
411A THR* 4.0 4.6 + - + -
412A ALA* 1.3 69.6 - - - +
414A PHE* 1.3 72.6 + - - +
415A THR* 3.7 17.8 + - + +
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Residues in contact with PHE 414 (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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319A ASN 3.2 4.7 + - - +
320A ASN* 4.2 15.5 - - - +
321A GLN* 4.8 4.2 + - - +
322A LEU* 4.0 21.9 - - + +
323A ARG* 3.8 18.6 - - + -
376A ILE* 3.5 22.4 - - + -
377A ALA 3.4 23.1 - - - -
378A GLU* 3.9 6.7 - - - -
384A THR* 3.3 37.0 - - + -
385A TYR 3.3 15.5 - - - -
386A TRP* 3.0 49.5 - + + -
413A ASN* 1.3 81.9 + - - +
415A THR* 1.3 59.4 + - - +
1375B VAL* 5.9 0.7 - - + -
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Residues in contact with THR 415 (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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322A LEU* 3.9 9.2 - - - -
384A THR* 3.3 7.5 + - - -
385A TYR* 2.8 41.7 + - + +
387A GLN* 3.7 37.2 - - + +
413A ASN* 3.7 19.4 + - - +
414A PHE* 1.3 76.2 - - - +
416A GLN* 1.3 75.7 + - - +
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Residues in contact with GLN 416 (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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322A LEU* 3.9 20.0 - - + +
382A HIS* 3.3 17.6 + - - +
383A LYS* 3.0 21.0 - - + +
384A THR* 3.7 14.6 - - - +
385A TYR* 3.7 11.8 + - - -
415A THR* 1.3 89.1 + - - +
417A TYR* 1.3 63.0 + - - +
1374B GLY 4.4 5.5 + - - +
1375B VAL* 4.2 15.0 - - - +
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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