Contacts of the helix formed by residues 335 - 345 (chain A) in PDB entry 5HG1
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 GLU 335 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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303A GLY* 3.8 4.7 - - - -
332A GLY 4.0 12.9 - - - +
333A ARG 4.4 6.1 - - - +
334A PHE* 1.3 75.5 - - - +
336A THR* 1.3 58.6 + - - +
337A LYS* 4.0 18.4 - - + +
338A ASP* 2.6 57.2 + - - +
339A ILE* 3.4 5.0 + - - +
358A ARG* 4.6 9.6 + - - -
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Residues in contact with THR 336 (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 GLY* 2.3 44.6 + - - +
300A MET 4.6 0.3 + - - -
302A MET* 3.6 12.7 - - + +
303A GLY* 3.2 16.5 + - - -
335A GLU* 1.3 72.0 - - - +
337A LYS* 1.3 64.4 + - - +
339A ILE* 2.8 29.3 + - + +
340A SER* 3.4 10.3 + - - +
415A SER* 6.5 0.4 - - - -
416A VAL* 4.4 12.6 - - + -
420A HIS* 6.3 2.2 - - + -
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Residues in contact with LYS 337 (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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335A GLU* 4.0 19.9 - - + +
336A THR* 1.3 78.4 - - - +
338A ASP* 1.3 67.0 + - - +
340A SER* 3.4 15.6 + - - -
341A ASP* 2.7 46.5 + - - +
419A LYS* 6.4 1.8 - - + -
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Residues in contact with ASP 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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333A ARG 3.9 0.9 - - - +
334A PHE* 4.0 7.8 - - + -
335A GLU* 2.6 49.6 + - - +
337A LYS* 1.3 77.1 + - - +
339A ILE* 1.3 59.3 + - - +
341A ASP* 3.3 9.8 + - - +
342A ILE* 2.7 45.5 + - + +
355A VAL* 3.8 15.7 - - + +
358A ARG* 2.6 34.5 + - - -
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Residues in contact with ILE 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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302A MET* 3.4 62.8 - - + +
303A GLY* 3.4 6.3 - - - +
306A VAL* 4.1 4.3 - - + -
334A PHE* 4.2 8.7 - - + -
335A GLU 4.0 6.3 - - - +
336A THR* 2.8 14.8 + - + +
338A ASP* 1.3 76.4 - - - +
340A SER* 1.3 61.5 + - - +
342A ILE* 3.7 1.7 + - - +
343A GLU* 3.2 24.5 + - - +
375A CYS* 3.7 47.3 - - + +
378A VAL* 4.8 2.0 - - + -
379A SER* 4.5 6.1 - - - -
420A HIS* 4.5 6.7 - - + +
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Residues in contact with SER 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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336A THR* 3.4 11.1 + - - +
337A LYS* 3.4 11.8 + - - -
338A ASP 3.1 0.6 - - - -
339A ILE* 1.3 75.3 - - - +
341A ASP* 1.3 63.2 + - - +
343A GLU 3.2 1.6 + - - -
344A GLY* 2.8 30.1 + - - -
419A LYS* 4.5 7.8 - - - +
420A HIS* 3.7 27.5 + - - +
421A PRO* 3.7 21.7 - - - +
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Residues in contact with ASP 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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337A LYS* 2.7 47.7 + - - +
338A ASP* 3.3 13.1 + - - +
340A SER* 1.3 80.2 - - - +
342A ILE* 1.3 65.2 + - + +
343A GLU 3.1 1.0 + - - -
344A GLY* 3.2 9.5 + - - -
345A GLU* 4.0 10.2 + - - +
348A GLY* 4.5 0.3 - - - -
351A LYS* 3.1 39.4 + - + +
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Residues in contact with ILE 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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334A PHE* 4.4 14.4 - - + -
338A ASP* 2.7 46.1 + - + +
339A ILE* 4.0 4.0 - - - +
341A ASP* 1.3 76.8 - - + +
343A GLU* 1.3 60.9 + - - +
348A GLY* 3.5 25.5 - - - +
351A LYS* 4.2 1.1 - - - -
352A ALA* 3.6 29.6 - - + +
355A VAL* 4.2 19.5 - - + -
371A THR* 4.8 2.2 - - + -
372A HIS* 3.1 48.8 + - + +
375A CYS* 4.3 13.7 - - + -
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Residues in contact with GLU 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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339A ILE* 3.2 13.1 + - - +
340A SER 3.2 3.6 + - - +
341A ASP 3.1 0.6 - - - -
342A ILE* 1.3 77.8 - - - +
344A GLY* 1.3 63.8 + - - +
345A GLU 3.7 2.7 - - - +
372A HIS* 3.7 22.1 - - + -
375A CYS* 2.9 14.7 - - + +
376A GLN* 2.6 49.5 + - + +
379A SER* 3.1 5.1 + - - -
420A HIS* 2.6 37.0 + - - -
421A PRO* 3.7 6.7 - - + -
422A HIS* 3.3 22.5 + - + -
426A ARG* 4.2 6.3 + - - -
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Residues in contact with GLY 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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340A SER 2.8 11.7 + - - -
341A ASP* 3.2 3.6 + - - -
343A GLU* 1.3 81.0 - - - +
345A GLU* 1.3 62.4 + - - +
421A PRO* 3.3 25.2 - - - +
422A HIS* 4.5 6.4 + - - -
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Residues in contact with GLU 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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341A ASP 4.0 4.6 + - - +
343A GLU 3.7 2.5 - - - +
344A GLY* 1.3 79.2 - - - +
346A LYS* 1.3 70.1 + - - +
347A ASP 3.0 23.9 + - - +
348A GLY* 3.5 13.5 + - - -
350A ARG* 3.9 10.3 + - - -
351A LYS* 3.0 47.2 - - - +
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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