Contacts of the helix formed by residues 312 - 322 (chain D) in PDB entry 2QJK
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 312 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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307D ALA 3.7 13.2 - - - +
308D PHE* 4.0 17.0 - - + -
309D THR* 3.0 34.5 + - - +
310D ALA 3.4 0.8 - - - -
311D ASP* 1.3 77.4 - - - +
313D TRP* 1.3 69.6 + - + +
314D VAL* 3.7 14.6 - - + +
315D VAL* 2.8 18.5 + - + +
316D GLN* 2.7 25.2 + - - +
394D LEU* 4.0 24.5 - - + -
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Residues in contact with TRP 313 (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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311D ASP 4.1 7.7 + - - -
312D VAL* 1.3 75.5 - - + +
314D VAL* 1.3 59.3 + - + +
316D GLN* 3.0 12.3 + - - +
317D ILE* 2.8 35.3 + - + +
391D TRP* 6.4 3.4 - + - -
313G TRP* 3.2 85.1 - + + +
316G GLN* 3.0 28.0 + - + -
317G ILE* 4.2 19.5 - - + -
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Residues in contact with VAL 314 (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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308D PHE* 5.8 2.5 - - + -
312D VAL* 3.3 9.8 - - + +
313D TRP* 1.3 79.6 - - + +
315D VAL* 1.3 66.9 - - - +
317D ILE* 3.4 15.2 - - + +
318D ALA* 2.8 23.9 + - + +
331D PHE* 3.5 29.6 - - + -
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Residues in contact with VAL 315 (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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308D PHE* 3.8 10.8 - - + -
309D THR 3.7 21.8 - - - +
310D ALA* 4.2 10.3 - - - +
312D VAL* 2.8 26.5 + - + +
314D VAL* 1.3 76.8 - - - +
316D GLN* 1.3 54.1 + - - +
318D ALA* 3.0 7.8 - - - +
319D ASN* 2.6 37.5 + - + +
326D ILE 4.6 0.7 - - - +
327D ASP 4.9 1.3 - - - -
328D ALA* 4.2 22.0 - - - +
331D PHE* 3.6 34.8 - - + -
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Residues in contact with GLN 316 (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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310D ALA 3.5 23.3 + - - +
311D ASP* 4.1 11.1 + - - +
312D VAL 2.7 22.9 + - - +
313D TRP* 3.2 14.6 - - - +
315D VAL* 1.3 70.5 - - - +
317D ILE* 1.3 72.5 + - - +
319D ASN* 2.8 11.5 + - - +
320D PHE* 2.8 22.0 + - - +
313G TRP* 3.5 28.0 + - + -
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Residues in contact with ILE 317 (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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313D TRP* 2.8 24.5 + - + +
314D VAL* 3.4 18.4 - - + +
316D GLN* 1.3 73.7 - - - +
318D ALA* 1.3 64.8 + - - +
320D PHE* 3.0 5.8 + - - +
321D ILE* 2.9 51.4 + - + +
313G TRP* 4.1 24.7 - - + -
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Residues in contact with ALA 318 (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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314D VAL* 2.8 23.1 + - + +
315D VAL* 3.0 9.2 - - - +
317D ILE* 1.3 77.3 - - - +
319D ASN* 1.3 64.1 + - - +
321D ILE* 3.4 6.2 + - - +
322D SER* 2.9 27.8 + - - -
326D ILE* 4.3 12.0 - - + +
331D PHE* 4.2 20.9 - - + -
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Residues in contact with ASN 319 (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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315D VAL* 2.6 19.9 + - + +
316D GLN* 2.8 14.9 + - - +
318D ALA* 1.3 72.3 - - - +
320D PHE* 1.3 65.3 - - - +
322D SER* 3.0 6.4 + - - -
324D GLY* 2.7 55.0 + - - +
326D ILE 3.6 15.6 + - - +
327D ASP* 4.4 12.8 - - - +
328D ALA 5.7 0.2 - - - +
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Residues in contact with PHE 320 (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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316D GLN 2.8 14.2 + - - +
317D ILE* 3.0 9.8 + - - +
319D ASN* 1.3 78.2 - - - +
321D ILE* 1.3 74.9 + - + +
323D PHE* 2.8 28.6 + - - -
324D GLY 4.9 0.4 - - - +
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Residues in contact with ILE 321 (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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317D ILE* 2.9 44.4 + - + +
318D ALA* 3.8 5.2 - - - +
320D PHE* 1.3 86.9 - - + +
322D SER* 1.3 57.1 + - - +
323D PHE* 3.2 20.9 - - - -
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Residues in contact with SER 322 (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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318D ALA 2.9 20.5 + - - -
319D ASN 3.0 7.1 + - - -
321D ILE* 1.3 74.8 - - - +
323D PHE* 1.3 74.8 + - - +
325D ILE* 3.2 20.7 + - - +
326D ILE* 2.9 47.0 + - - +
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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