Contacts of the helix formed by residues 315 - 324 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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283E GLN* 4.3 6.2 - - - +
313E SER 3.9 2.0 + - - -
314E GLU* 1.3 72.2 - - - +
316E PRO* 1.3 77.3 - - - +
317E TRP* 3.2 19.7 + - - +
318E GLU* 3.7 30.5 + - + +
319E GLN* 3.2 23.8 + - - +
338E TYR* 3.7 16.6 + - - -
258H ARG* 2.9 34.5 - - - +
259H ASN* 4.0 10.0 - - + +
260H PRO* 5.8 0.4 - - - +
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Residues in contact with PRO 316 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279E VAL* 5.4 4.3 - - + -
280E ASN 4.9 0.9 - - - +
283E GLN* 3.8 41.3 - - + +
284E LEU* 3.9 22.2 - - + +
287E ALA* 3.5 24.5 - - + -
289E PHE* 3.9 5.0 - - + -
310E TRP* 4.1 14.4 - - + -
314E GLU 3.4 9.4 - - - +
315E ASP* 1.3 90.2 - - - +
317E TRP* 1.3 56.4 + - + +
319E GLN* 3.3 2.3 + - - +
320E HIS* 2.9 28.9 + - - +
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Residues in contact with TRP 317 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283E GLN* 5.3 3.1 + - - -
286E ARG* 3.1 35.0 - - + +
287E ALA* 3.8 28.6 - - + +
315E ASP* 3.2 14.8 + - - +
316E PRO* 1.3 79.1 - - + +
318E GLU* 1.3 57.9 + - - +
320E HIS* 3.3 5.2 - - - +
321E ALA* 2.9 31.2 + - - +
329E TYR* 3.5 17.9 - + - -
330E LEU* 3.7 31.9 - - + +
333E GLN* 3.5 33.0 - - + -
334E LYS* 3.7 32.6 - - + +
338E TYR* 3.4 18.4 + - + +
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Residues in contact with GLU 318 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315E ASP* 3.3 29.2 + - + +
316E PRO 3.3 0.8 - - - -
317E TRP* 1.3 78.7 - - - +
319E GLN* 1.3 60.2 + - + +
321E ALA* 3.4 1.0 + - - -
322E LYS* 2.7 37.0 + - + +
338E TYR* 3.2 12.1 + - - +
342E ILE* 3.8 23.6 - - + +
345E THR* 6.0 2.3 - - - +
258H ARG* 3.4 28.3 + - - +
299H LYS* 3.8 30.4 + - - +
304H GLY* 4.4 4.9 - - - +
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Residues in contact with GLN 319 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307E LEU* 3.6 21.1 - - + +
310E TRP* 3.7 16.8 - - + -
314E GLU* 3.0 33.1 + - + +
315E ASP 3.2 14.1 + - - +
316E PRO 3.7 5.4 - - - +
318E GLU* 1.3 83.5 + - - +
320E HIS* 1.3 66.0 + - - +
322E LYS* 3.5 19.0 - - - +
323E TRP* 3.1 36.7 + - - +
403E 1AQ 3.4 25.0 + - + +
299H LYS* 5.6 4.4 - - - +
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Residues in contact with HIS 320 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287E ALA* 2.8 29.7 + - - +
289E PHE* 3.3 20.1 - + + -
300E CYS* 3.4 15.7 - - + +
303E CYS* 3.5 4.0 - - - -
307E LEU* 4.2 2.8 - - - +
316E PRO 2.9 13.9 + - - +
317E TRP* 3.3 13.6 - - - +
319E GLN* 1.3 75.6 - - - +
321E ALA* 1.3 54.2 + - - +
324E TYR* 2.7 52.4 + + + +
327E CYS* 3.4 8.9 - - + -
329E TYR* 4.7 4.5 - + - -
330E LEU* 4.0 14.7 - - + +
401E ZN 2.1 37.3 - - - -
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Residues in contact with ALA 321 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317E TRP 2.9 15.8 + - - +
318E GLU 3.9 3.1 - - - +
320E HIS* 1.3 74.5 - - - +
322E LYS* 1.3 67.9 + - - +
323E TRP 3.4 0.2 + - - -
325E PRO* 3.7 20.9 - - - +
330E LEU* 3.7 28.7 - - + +
338E TYR* 4.1 17.3 - - + -
339E ILE* 4.5 10.1 - - + +
342E ILE* 3.9 16.6 - - + +
343E HIS* 5.4 2.6 + - - +
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Residues in contact with LYS 322 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343D HIS* 3.1 19.2 + - - -
318E GLU* 2.7 25.2 + - + +
319E GLN* 3.5 28.7 - - - +
320E HIS 3.2 0.2 - - - -
321E ALA* 1.3 74.2 - - - +
323E TRP* 1.3 84.4 + - + +
342E ILE* 3.5 13.4 - - + +
346E HIS* 3.9 40.7 + - + +
349E GLU* 5.1 11.2 + - - +
402E ZN 3.2 11.5 - - - -
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Residues in contact with TRP 323 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343D HIS* 3.2 28.1 - + - -
344D LEU* 3.7 9.6 - - + +
347D SER* 4.9 11.7 - - - -
307E LEU* 3.6 22.0 - - + -
319E GLN* 3.1 22.8 + - - +
322E LYS* 1.3 103.8 - - + +
324E TYR* 1.3 88.8 - - + +
325E PRO* 3.4 3.8 - - - -
346E HIS* 4.0 25.6 - + - -
349E GLU* 4.8 8.7 - - - -
403E 1AQ 3.4 70.0 + - + -
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Residues in contact with TYR 324 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341B ASN* 6.1 0.9 - - - -
345B THR* 5.4 9.8 + - - +
340D ASN* 3.3 20.9 - - + +
344D LEU* 4.9 12.1 - - + -
289E PHE* 5.8 1.3 - + - -
303E CYS* 3.9 19.7 - - + -
305E GLY* 3.4 28.3 - - - -
306E GLY* 2.9 36.1 + - - -
307E LEU* 4.1 9.9 - - + -
320E HIS* 2.7 27.8 + + + +
323E TRP* 1.3 94.2 - - + +
325E PRO* 1.3 61.6 - - - +
326E GLY 3.1 7.0 + - - -
327E CYS* 3.4 12.0 + - - +
330E LEU* 3.6 10.9 - - - +
403E 1AQ 3.4 21.4 + - - +
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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