Contacts of the helix formed by residues 315 - 324 (chain D) in PDB entry 4HY0
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 ASP 315 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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258A ARG* 3.9 20.4 - - - +
283D GLN* 4.4 7.1 + - - +
310D TRP* 4.4 0.9 - - - -
313D SER 5.5 0.4 - - - +
314D GLU* 1.3 74.4 - - - +
316D PRO* 1.3 68.8 - - - +
317D TRP* 2.6 42.2 + - - +
318D GLU* 3.0 31.7 + - - +
319D GLN* 3.1 27.9 + - - +
338D TYR* 4.9 2.4 + - - -
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Residues in contact with PRO 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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279D VAL* 5.5 2.9 - - + -
283D GLN* 3.2 61.0 - - + +
284D LEU* 3.6 26.5 - - + +
287D ALA* 3.6 10.5 - - + -
289D PHE* 3.6 7.2 - - + -
310D TRP* 3.9 13.7 - - + -
314D GLU 3.8 5.1 - - - +
315D ASP* 1.3 86.9 - - - +
317D TRP* 1.3 58.1 + - + +
319D GLN* 3.4 2.1 + - - +
320D HIS* 2.9 28.8 + - - +
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Residues in contact with TRP 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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283D GLN* 5.3 6.0 + - + +
286D ARG* 3.5 32.1 - - + +
287D ALA* 3.7 34.5 - - + +
315D ASP* 2.6 18.5 + - - +
316D PRO* 1.3 73.5 - - + +
318D GLU* 1.3 65.9 + - - +
320D HIS* 3.2 5.6 + - - +
321D ALA* 3.0 23.2 + - - +
329D TYR* 3.8 4.9 - + - -
330D LEU* 3.3 44.1 - - + +
333D GLN* 3.5 34.3 - - + -
334D LYS* 3.4 35.1 - - + +
338D TYR* 3.5 17.1 + - + +
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Residues in contact with GLU 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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258A ARG* 5.3 7.8 + - - +
299A LYS* 2.7 33.9 + - - -
315D ASP* 3.0 28.7 + - + +
317D TRP* 1.3 78.2 - - - +
319D GLN* 1.3 69.1 + - - +
321D ALA* 3.4 2.6 + - - +
322D LYS* 2.9 32.4 + - + +
338D TYR* 3.2 12.2 + - - +
342D ILE* 3.7 24.9 - - + +
345D THR* 5.8 3.6 - - - +
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Residues in contact with GLN 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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307D LEU* 3.8 20.2 - - + +
310D TRP* 3.6 19.1 - - + -
314D GLU* 3.1 33.1 + - - +
315D ASP 3.1 18.8 + - - +
316D PRO 3.7 4.3 - - - +
317D TRP 3.2 0.2 - - - -
318D GLU* 1.3 88.3 + - - +
320D HIS* 1.3 66.0 + - - +
322D LYS* 3.4 13.5 + - - +
323D TRP* 3.2 48.2 + - + +
403D 1AQ 4.0 10.5 + - + +
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Residues in contact with HIS 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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287D ALA 3.2 23.1 + - - -
289D PHE* 3.6 16.1 - + + -
300D CYS* 3.2 17.9 - - + +
303D CYS* 3.2 4.6 - - - -
307D LEU* 4.2 2.6 - - - +
316D PRO 2.9 14.9 + - - +
317D TRP* 3.2 11.6 + - - +
319D GLN* 1.3 77.0 - - - +
321D ALA* 1.3 56.8 + - - +
324D TYR* 2.8 51.4 + + + +
327D CYS* 3.6 10.5 - - + +
329D TYR* 4.9 2.0 - + - -
330D LEU* 4.3 16.7 - - + +
401D ZN 2.0 39.0 - - - -
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Residues in contact with ALA 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 TRP 3.0 16.1 + - - +
318D GLU 3.7 4.0 - - - +
320D HIS* 1.3 73.8 - - - +
322D LYS* 1.3 65.9 + - - +
323D TRP 3.4 0.2 + - - -
325D PRO* 3.6 25.3 - - - +
330D LEU* 3.7 18.8 - - + +
338D TYR* 4.1 10.5 - - + -
339D ILE* 4.7 9.5 - - - +
342D ILE* 3.7 29.0 - - + +
343D HIS* 5.5 1.0 + - - +
402D ZN 4.3 2.9 - - - -
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Residues in contact with LYS 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 GLU* 2.9 20.3 + - + +
319D GLN* 3.8 24.0 - - - +
320D HIS 3.3 0.2 - - - -
321D ALA* 1.3 78.6 - - - +
323D TRP* 1.3 92.4 + - + +
342D ILE* 4.1 12.6 - - + -
346D HIS* 3.6 36.6 - - + +
349D GLU* 4.0 17.0 + - - -
350D GLU* 4.1 11.0 + - - +
402D ZN 3.3 9.4 - - - -
403D 1AQ 5.6 0.7 - - - -
343E HIS* 2.9 20.8 + - - -
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Residues in contact with TRP 323 (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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307D LEU* 3.6 18.6 - - + -
319D GLN* 3.2 33.5 + - - +
322D LYS* 1.3 110.7 - - + +
324D TYR* 1.3 89.4 + - + +
325D PRO* 3.7 4.2 - - - +
346D HIS* 4.6 7.6 - - - -
350D GLU* 4.1 20.9 - - - -
403D 1AQ 3.3 74.9 + - + -
340E ASN* 4.4 0.2 - - - +
343E HIS* 3.5 20.9 - + - -
344E LEU* 3.9 11.2 - - + +
347E SER* 4.6 15.3 - - - -
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Residues in contact with TYR 324 (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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345C THR* 5.4 7.4 + - - +
289D PHE* 5.9 0.7 - + - -
303D CYS* 3.9 16.4 - - - -
305D GLY* 3.4 32.1 - - - -
306D GLY 2.6 33.8 + - - -
307D LEU* 3.6 19.3 - - + -
319D GLN 5.0 0.7 - - - -
320D HIS* 2.8 35.9 + + + +
323D TRP* 1.3 91.5 - - + +
325D PRO* 1.3 63.5 - - - +
326D GLY 3.1 6.7 + - - -
327D CYS 3.6 5.7 + - - -
330D LEU* 3.9 2.4 - - - +
403D 1AQ 3.2 21.8 + - - +
340E ASN* 3.2 22.4 - - + +
344E LEU* 5.1 9.0 - - + -
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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