Contacts of the helix formed by residues 301 - 312 (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 ASN 301 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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296A ASN 3.0 23.2 + - - -
297A LEU* 3.7 4.2 - - - -
298A SER* 2.9 37.1 + - - +
300A GLU* 1.3 78.0 - - + +
302A ALA* 1.3 63.5 + - - +
303A ALA 3.4 2.2 - - - -
304A GLU* 3.1 17.6 + - + +
305A ILE* 2.9 45.8 + - + +
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Residues in contact with ALA 302 (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 9.9 - - + -
298A SER 3.0 17.1 + - - +
299A VAL 3.6 8.6 + - - +
300A GLU 3.6 0.2 - - - -
301A ASN* 1.3 80.6 - - - +
303A ALA* 1.4 59.1 + - - +
305A ILE* 3.2 3.1 + - - +
306A LEU* 2.9 28.2 + - - +
321A ALA* 4.3 2.9 - - - +
324A PHE* 3.7 19.5 - - + -
325A ILE* 3.7 25.5 - - + +
332A VAL* 4.3 4.0 - - + -
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Residues in contact with ALA 303 (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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299A VAL 5.0 0.8 + - - -
300A GLU 5.5 0.2 + - - -
301A ASN 3.4 0.2 - - - -
302A ALA* 1.4 78.1 - - - +
304A GLU* 1.3 57.8 + - - +
306A LEU* 3.2 4.5 + - - +
307A ILE* 3.0 32.3 + - - +
325A ILE* 4.1 10.6 - - + +
332A VAL* 4.9 4.0 - - + +
335A THR* 5.1 1.3 + - - +
337A GLY* 3.5 10.8 - - - +
338A TRP* 3.5 41.5 - - + +
341A MET* 3.7 17.0 - - + +
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Residues in contact with GLU 304 (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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300A GLU 3.4 20.1 - - - +
301A ASN* 3.1 14.2 + - + +
303A ALA* 1.3 78.1 - - - +
305A ILE* 1.3 57.7 + - + +
307A ILE* 3.3 15.7 + - + +
308A LEU* 3.0 35.5 + - + +
337A GLY* 4.3 23.3 + - - +
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Residues in contact with ILE 305 (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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296A ASN 6.1 0.7 - - - -
297A LEU* 3.8 22.0 - - + -
301A ASN* 2.9 43.1 + - + +
302A ALA 3.2 7.4 + - - +
304A GLU* 1.3 73.7 - - + +
306A LEU* 1.3 56.7 + - - +
308A LEU* 3.2 17.9 + - + +
309A ALA* 2.8 33.1 + - - +
317A LEU* 3.8 33.8 - - + +
321A ALA* 4.2 4.7 - - + -
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Residues in contact with LEU 306 (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 2.9 14.4 + - - +
303A ALA 3.4 8.3 - - - +
305A ILE* 1.3 77.2 - - - +
307A ILE* 1.3 61.8 + - - +
309A ALA* 3.3 1.6 + - - +
310A ASP* 2.9 22.9 + - - +
318A LYS* 3.7 40.2 - - + +
321A ALA* 4.0 11.2 - - + +
322A VAL* 3.7 23.6 - - + -
325A ILE* 3.8 19.3 - - + -
341A MET* 4.0 17.3 - - + -
348A LEU* 4.1 28.9 - - + +
351A GLU* 6.2 0.2 - - + -
352A ALA* 5.0 3.6 - - + -
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Residues in contact with ILE 307 (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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303A ALA 3.0 18.5 + - - +
304A GLU* 3.6 17.3 - - + +
305A ILE 3.3 0.2 - - - -
306A LEU* 1.3 77.2 - - - +
308A LEU* 1.3 64.3 + - + +
310A ASP* 3.3 2.9 + - - +
311A LEU* 2.9 30.0 + - + +
337A GLY 5.1 1.8 - - - +
340A SER* 5.7 0.7 - - - -
341A MET* 3.8 30.1 - - + +
344A SER* 4.2 4.0 - - - +
345A HIS* 3.7 45.0 - - + +
348A LEU* 3.7 11.4 - - + +
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Residues in contact with LEU 308 (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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304A GLU* 3.0 24.4 + - + +
305A ILE* 3.8 18.4 - - + +
307A ILE* 1.3 78.4 - - + +
309A ALA* 1.3 66.5 + - - +
311A LEU* 3.4 20.4 + - + -
312A HIS* 3.1 38.7 + - + +
317A LEU* 5.4 4.0 - - + -
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Residues in contact with ALA 309 (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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305A ILE 2.8 20.5 + - - +
306A LEU* 3.7 4.5 - - - +
308A LEU* 1.3 73.0 - - - +
310A ASP* 1.3 58.2 + - - +
312A HIS 3.4 0.3 + - - -
313A SER 3.0 8.0 + - - -
314A ALA* 2.9 37.4 + - - +
317A LEU* 3.8 18.3 - - + +
318A LYS* 3.5 38.7 - - - +
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Residues in contact with ASP 310 (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 2.9 17.0 + - - +
307A ILE 3.6 4.8 - - - +
309A ALA* 1.3 77.4 - - - +
311A LEU* 1.3 64.6 + - - +
313A SER* 3.1 17.7 + - - +
318A LYS* 2.8 32.8 + - - +
345A HIS* 4.9 4.0 - - - -
347A HIS* 3.4 21.6 + - - -
348A LEU* 3.7 25.3 - - + +
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Residues in contact with LEU 311 (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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307A ILE* 2.9 22.1 + - + +
308A LEU* 3.7 19.7 - - + +
309A ALA 3.3 0.2 - - - -
310A ASP* 1.3 78.0 + - - +
312A HIS* 1.3 86.5 + - + +
313A SER* 3.4 2.6 + - - -
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Residues in contact with HIS 312 (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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308A LEU* 3.1 33.5 + - + +
309A ALA 4.4 0.7 - - - +
311A LEU* 1.3 102.6 + - + +
313A SER* 1.3 70.2 + - - +
314A ALA* 3.1 10.8 + - + +
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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