Contacts of the helix formed by residues 337 - 346 (chain A) in PDB entry 5HAN
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 337 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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306A ALA* 6.1 0.9 - - - -
323A THR 4.8 7.0 - - - +
326A MET* 3.7 24.3 + - + +
333A GLY* 3.5 10.7 - - - -
334A GLU* 2.9 42.0 + - - +
336A ALA* 1.4 73.9 - - - +
338A ARG* 1.3 63.1 + - - +
339A ALA 3.1 2.2 - - - -
340A ILE* 2.9 45.3 + - + +
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Residues in contact with ARG 338 (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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326A MET* 3.7 20.4 - - - -
335A ALA* 3.2 28.9 + - - +
336A ALA* 3.0 13.6 + - - +
337A ASP* 1.3 76.7 - - - +
339A ALA* 1.4 65.6 + - + +
341A ALA* 3.1 14.3 + - - +
342A TYR* 3.1 37.8 + - + -
383A ASN* 2.5 46.6 + - - +
384A LEU* 4.2 9.2 - - + -
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Residues in contact with ALA 339 (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 PHE* 4.1 9.6 - - + -
336A ALA 3.2 14.7 + - - +
337A ASP 3.1 0.6 - - - -
338A ARG* 1.4 81.0 - - + +
340A ILE* 1.3 60.3 + - + +
342A TYR* 3.5 11.0 + - - +
343A MET* 3.1 23.6 + - - +
350A ASP 4.8 13.1 - - - +
351A GLY* 6.3 0.4 - - - -
352A PRO* 6.5 0.4 - - + -
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Residues in contact with ILE 340 (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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289A ARG* 5.9 0.2 - - - +
306A ALA* 4.1 14.8 - - + -
307A PHE* 3.8 44.0 - - + +
310A SER* 3.3 34.1 - - - +
323A THR* 4.1 25.6 - - + +
337A ASP* 2.9 38.7 + - + +
339A ALA* 1.3 75.6 - - + +
341A ALA* 1.4 63.9 + - - +
343A MET* 3.2 4.4 + - + +
344A ILE* 3.2 22.7 + - - +
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Residues in contact with ALA 341 (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 THR* 4.9 1.3 - - - +
326A MET* 4.0 13.8 - - + +
337A ASP 3.7 1.4 + - - -
338A ARG 3.1 10.2 + - - +
340A ILE* 1.4 78.9 - - - +
342A TYR* 1.3 61.4 + - + +
344A ILE* 3.3 11.6 - - - +
345A THR* 2.9 32.8 + - - +
366A PRO* 4.1 20.2 - - + -
384A LEU* 3.8 23.1 - - + -
386A HIS* 5.2 2.5 - - - +
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Residues in contact with TYR 342 (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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338A ARG* 3.1 45.6 + - + -
339A ALA* 3.9 9.0 - - - +
340A ILE 3.3 0.2 - - - -
341A ALA* 1.3 78.2 - - + +
343A MET* 1.3 57.5 + - - +
345A THR* 3.6 7.9 - - - -
346A GLU* 3.0 49.9 + - + +
349A ALA* 3.9 8.5 - - + +
383A ASN 4.5 0.3 + - - -
384A LEU* 2.3 43.4 + - + +
385A GLY* 4.6 0.3 - - - -
386A HIS* 4.4 13.9 - + - -
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Residues in contact with MET 343 (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 PHE* 3.7 28.0 - - + -
311A LYS* 4.1 21.3 - - + +
314A ARG* 2.9 18.4 + - - -
339A ALA 3.1 14.9 + - - +
340A ILE 3.2 8.7 + - - +
342A TYR* 1.3 75.9 - - - +
344A ILE* 1.3 60.7 + - + +
349A ALA* 3.5 37.4 - - + +
350A ASP 3.7 1.8 - - - +
351A GLY* 3.6 22.0 - - - +
354A PHE 4.5 1.3 - - - +
356A GLN* 3.9 14.6 - - + -
358A TRP* 3.1 47.2 + - + -
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Residues in contact with ILE 344 (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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310A SER* 3.5 36.6 - - - +
311A LYS* 4.4 5.2 - - - +
314A ARG* 3.2 25.9 + - + +
321A ILE* 3.9 15.7 - - + -
323A THR* 3.7 29.6 - - + -
340A ILE 3.2 11.2 + - - +
341A ALA* 3.3 14.1 - - - +
343A MET* 1.3 79.0 - - + +
345A THR* 1.3 58.0 + - + +
364A THR* 2.8 51.6 + - + +
365A THR 4.1 0.4 - - - +
366A PRO* 4.0 10.3 - - + -
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Residues in contact with THR 345 (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 ARG* 4.1 1.4 + - - -
341A ALA* 2.9 22.9 + - + +
342A TYR* 3.5 9.7 + - - -
344A ILE* 1.3 79.3 - - - +
346A GLU* 1.3 81.2 + - - +
363A PRO* 3.4 21.6 - - + +
364A THR 3.6 17.9 - - - +
365A THR* 4.9 0.4 - - - -
366A PRO* 3.7 23.6 - - + -
386A HIS* 5.3 9.6 + - + +
388A ASN 5.9 0.4 - - - +
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Residues in contact with GLU 346 (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 ARG* 2.8 26.5 + - - -
342A TYR* 3.0 34.8 + - + +
343A MET 4.3 0.3 - - - +
345A THR* 1.3 99.1 + - - +
347A ASP* 1.3 63.2 + - - +
348A ALA 3.3 20.9 - - - +
349A ALA* 4.6 0.7 - - + -
358A TRP* 3.3 4.6 + - - -
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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