Contacts of the helix formed by residues 314 - 328 (chain A) in PDB entry 4HS2
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 ALA 314 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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309A ALA* 2.9 18.9 + - - +
312A HIS* 3.9 11.0 - - + +
313A SER* 1.3 72.7 - - - +
315A ASP* 1.3 60.1 + - - +
316A GLN 3.4 2.2 - - - -
317A LEU* 3.3 21.2 + - + +
318A LYS* 2.9 29.7 + - - +
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Residues in contact with ASP 315 (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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313A SER* 3.3 16.4 + - - +
314A ALA* 1.3 72.7 - - - +
316A GLN* 1.3 58.4 + - - +
318A LYS* 3.6 11.6 - - - +
319A THR* 2.9 35.0 + - - +
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Residues in contact with GLN 316 (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 ALA 3.4 0.4 - - - -
315A ASP* 1.3 78.1 - - - +
317A LEU* 1.3 58.0 + - - +
319A THR* 3.2 7.0 + - - -
320A GLN* 2.9 56.3 + - + +
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Residues in contact with LEU 317 (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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297A LEU* 5.3 6.5 - - + -
305A ILE* 3.8 29.4 - - + +
308A LEU* 5.4 3.1 - - + -
309A ALA* 3.8 22.2 - - + +
314A ALA* 3.3 18.5 + - + +
315A ASP 3.3 0.2 - - - -
316A GLN* 1.3 77.9 + - - +
318A LYS* 1.3 58.4 + - - +
320A GLN* 3.3 20.9 + - + +
321A ALA* 2.8 30.8 + - - +
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Residues in contact with LYS 318 (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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306A LEU* 3.7 14.6 - - + -
309A ALA* 3.5 15.1 - - + +
310A ASP* 2.8 37.9 + - - +
314A ALA 2.9 18.1 + - - +
315A ASP* 3.6 12.6 - - - +
317A LEU* 1.3 76.7 - - - +
319A THR* 1.3 58.6 + - - +
321A ALA* 3.3 2.3 + - - +
322A VAL* 2.9 32.5 + - + +
348A LEU* 3.9 12.8 - - - +
351A GLU* 2.9 41.1 + - - +
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Residues in contact with THR 319 (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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315A ASP* 2.9 17.6 + - - +
316A GLN* 3.6 6.1 - - - -
318A LYS* 1.3 78.5 - - - +
320A GLN* 1.3 56.7 + - + +
322A VAL* 3.4 5.5 + - - +
323A ASP* 2.9 48.0 + - - +
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Residues in contact with GLN 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A LEU* 3.7 14.1 - - + +
316A GLN* 2.9 55.5 + - + +
317A LEU* 3.3 19.5 + - - +
319A THR* 1.3 77.1 - - + +
321A ALA* 1.3 56.7 + - - +
323A ASP* 3.4 5.9 + - - +
324A PHE* 2.9 30.7 + - - +
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Residues in contact with ALA 321 (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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297A LEU* 4.0 15.2 - - + +
302A ALA 4.3 2.2 - - - +
305A ILE* 4.2 12.6 - - + -
306A LEU* 4.0 33.9 - - + +
317A LEU 2.8 17.2 + - - +
318A LYS 3.7 4.0 - - - +
320A GLN* 1.3 74.5 - - - +
322A VAL* 1.3 60.9 + - - +
324A PHE* 3.3 2.1 + - - +
325A ILE* 2.9 36.4 + - - +
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Residues in contact with VAL 322 (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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306A LEU* 3.7 26.9 - - + -
318A LYS* 2.9 25.4 + - + +
319A THR* 3.9 5.4 - - - +
321A ALA* 1.3 73.9 - - - +
323A ASP* 1.3 60.8 + - - +
325A ILE* 3.3 7.1 + - - +
326A ASN* 2.9 35.4 + - - +
351A GLU* 4.6 16.4 - - + +
352A ALA* 4.0 15.5 - - - -
355A SER* 3.6 33.7 - - - +
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Residues in contact with ASP 323 (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 THR* 2.9 37.1 + - - +
320A GLN* 3.8 6.2 - - - +
322A VAL* 1.3 77.1 - - - +
324A PHE* 1.3 57.7 + - - +
326A ASN* 3.4 6.9 + - - +
327A TYR* 3.0 30.5 + - - +
355A SER* 4.1 13.3 + - - -
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Residues in contact with PHE 324 (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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297A LEU* 3.8 33.2 - - + -
298A SER* 3.5 38.6 - - - -
299A VAL* 3.7 12.1 - - + -
302A ALA* 3.7 17.7 - - + -
320A GLN 2.9 19.0 + - - +
321A ALA 3.6 3.8 - - - +
323A ASP* 1.3 74.9 - - - +
325A ILE* 1.3 62.2 + - - +
327A TYR* 3.2 4.4 + - - -
328A HIS* 2.9 69.7 + + + +
332A VAL* 4.5 0.4 - - + -
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Residues in contact with ILE 325 (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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302A ALA* 3.7 38.6 - - + +
303A ALA* 4.1 7.6 - - + +
306A LEU* 3.8 29.4 - - + -
321A ALA 2.9 21.2 + - - +
322A VAL* 3.3 5.1 + - - +
324A PHE* 1.3 74.2 - - - +
326A ASN* 1.3 64.3 + - - +
328A HIS 3.2 1.2 + - - -
329A ALA* 2.8 36.6 + - + -
332A VAL* 3.9 20.4 - - + -
333A LEU* 5.2 2.0 - - + -
338A TRP* 3.9 27.8 - - + -
352A ALA* 5.0 4.7 - - + -
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Residues in contact with ASN 326 (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 VAL* 2.9 27.0 + - - +
323A ASP* 3.7 8.2 + - - +
325A ILE* 1.3 79.6 - - - +
327A TYR* 1.3 61.3 + - - +
328A HIS 3.4 0.5 + - - -
329A ALA* 3.5 16.0 + - - +
352A ALA* 3.6 20.6 - - - +
355A SER* 3.3 25.7 + - - -
356A LEU* 3.5 47.6 - - + +
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Residues in contact with TYR 327 (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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323A ASP 3.0 18.8 + - - +
324A PHE* 3.2 5.8 + - - +
326A ASN* 1.3 78.1 - - - +
328A HIS* 1.3 82.9 + + + +
329A ALA 3.9 0.3 + - - -
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Residues in contact with HIS 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A VAL* 4.1 15.5 - - + +
324A PHE* 2.9 61.3 + + + +
325A ILE 3.3 2.5 - - - -
327A TYR* 1.3 104.2 + + + +
329A ALA* 1.3 62.2 - - - +
330A SER* 3.3 4.3 - - - -
331A ASP* 3.0 14.4 + - + -
332A VAL* 2.9 31.1 + - + +
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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