Contacts of the strand formed by residues 328 - 333 (chain D) in PDB entry 1QK1
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 VAL 328 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122D LEU* 3.9 24.0 - - + -
291D HIS* 4.8 1.8 - - + -
292D ILE 3.3 8.5 - - - +
293D LYS* 3.7 24.2 - - + -
315D ARG 5.0 0.2 - - - +
316D GLY* 5.4 0.5 - - - -
317D THR* 2.7 48.3 + - + +
323D ALA 5.2 0.9 + - - +
324D ALA* 4.4 9.0 - - + +
325D THR* 4.6 15.7 - - + +
326D GLY* 3.2 10.6 - - - +
327D GLY* 1.3 77.9 - - - +
329D PHE* 1.3 71.1 + - - +
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Residues in contact with PHE 329 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290D VAL 3.4 0.9 - - - +
291D HIS* 3.2 9.2 - - - +
292D ILE* 2.9 35.5 + - + +
294D LEU* 4.3 9.4 - - + -
298D SER* 3.4 35.4 - - - -
303D PHE* 4.5 10.5 - + - -
314D LYS* 3.9 31.9 - - + -
315D ARG 3.9 13.7 - - - +
316D GLY* 5.9 0.4 - - - -
317D THR* 4.4 2.9 - - - -
327D GLY* 3.5 26.7 - - - -
328D VAL* 1.3 78.7 - - - +
330D ASP* 1.3 60.5 + - - +
331D ILE* 3.8 20.5 + - + -
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Residues in contact with ASP 330 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287D ARG* 2.9 37.4 + - - -
289D GLY* 5.1 1.2 - - - -
290D VAL 3.4 7.5 + - - +
291D HIS* 3.5 25.8 + - + -
313D GLN* 3.5 1.4 - - - +
314D LYS* 3.3 4.7 - - - -
315D ARG* 3.1 50.7 + - + +
316D GLY 3.7 9.6 + - - +
329D PHE* 1.3 72.0 - - - +
331D ILE* 1.3 65.9 + - - +
332D SER* 4.3 0.9 + - - -
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Residues in contact with ILE 331 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289D GLY* 3.0 22.7 - - - -
290D VAL* 3.0 21.6 + - + +
292D ILE* 3.7 26.7 - - + -
294D LEU* 5.1 0.2 - - + -
303D PHE* 4.7 11.0 - - + -
307D LEU* 4.7 4.3 - - + -
312D LEU* 3.9 33.9 - - + -
313D GLN 3.4 6.1 - - - +
314D LYS* 3.4 29.8 - - + -
329D PHE* 4.0 9.2 - - + -
330D ASP* 1.3 75.3 - - - +
332D SER* 1.3 63.7 + - - +
348D VAL* 5.2 1.6 - - - +
352D VAL* 4.6 6.7 - - + -
355D LEU* 4.1 18.4 - - + -
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Residues in contact with SER 332 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287D ARG* 3.2 43.9 + - - -
288D ALA 3.1 20.2 - - - -
289D GLY* 3.9 0.9 - - - -
312D LEU* 3.4 10.8 - - - -
313D GLN* 2.9 45.5 + - - +
315D ARG* 4.6 0.5 + - - -
330D ASP* 4.3 0.7 + - - -
331D ILE* 1.3 77.1 - - - +
333D ASN* 1.3 61.6 + - - +
348D VAL* 4.8 1.1 - - - -
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Residues in contact with ASN 333 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286D LEU* 2.9 26.2 + - - +
287D ARG* 3.5 1.9 - - - -
288D ALA* 2.7 37.5 + - - +
311D ARG 4.0 5.6 - - - -
312D LEU* 4.2 1.1 - - - -
313D GLN* 3.4 6.3 + - - -
332D SER* 1.3 75.4 + - - +
334D LEU* 1.3 59.3 + - - +
335D ASP 2.8 27.8 + - - +
336D ARG* 2.9 25.3 + - - +
344D LEU* 4.1 20.0 - - + +
347D LEU* 4.7 7.4 - - + -
348D VAL* 3.6 19.8 - - + +
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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