Contacts of the helix formed by residues 335 - 346 (chain E) in PDB entry 3G76
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 GLY 335 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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331E LEU* 2.9 22.7 + - - -
332E GLU 4.7 1.0 + - - -
334E LYS* 1.3 79.1 - - - +
336E GLN* 1.3 60.1 + - - -
337E GLU 3.2 2.9 - - - -
338E TYR* 2.9 24.5 + - - +
339E ILE* 3.5 5.4 + - - +
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Residues in contact with GLN 336 (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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336A GLN* 3.0 38.2 + - + +
340A ASN* 3.7 17.0 + - - +
325E PRO 4.3 1.2 + - - -
331E LEU* 3.4 29.8 - - + +
335E GLY* 1.3 69.7 - - - -
337E GLU* 1.3 57.8 + - - +
338E TYR 3.2 0.2 - - - -
339E ILE* 3.3 21.9 + - - +
340E ASN* 2.8 60.0 + - - +
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Residues in contact with GLU 337 (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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335E GLY 3.1 1.8 + - - -
336E GLN* 1.3 77.0 - - - +
338E TYR* 1.3 53.4 + - - +
340E ASN* 3.2 9.4 + - + +
341E ASN* 2.7 62.9 + - - +
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Residues in contact with TYR 338 (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* 3.9 3.8 + - - -
317E TRP* 3.2 43.8 - - - +
318E GLU* 3.2 6.1 + - - -
321E ALA* 4.3 4.9 - - + -
330E LEU* 4.4 4.3 - - + -
334E LYS* 3.3 60.3 + - + +
335E GLY 2.9 11.7 + - - +
337E GLU* 1.3 76.4 - - - +
339E ILE* 1.3 69.3 + - - +
341E ASN* 2.9 19.9 + - + +
342E ILE* 2.9 38.1 + - + +
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Residues in contact with ILE 339 (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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340A ASN* 4.4 5.8 - - - +
321E ALA* 4.3 10.3 - - + -
325E PRO* 3.9 23.8 - - + +
327E CYS 5.2 0.4 - - - +
330E LEU* 3.8 42.0 - - + -
331E LEU* 4.2 20.4 - - + -
334E LYS* 5.3 0.4 - - + -
335E GLY 3.5 5.1 + - - +
336E GLN* 3.3 35.6 + - - +
338E TYR* 1.3 84.5 - - + +
340E ASN* 1.3 66.7 + - - +
342E ILE* 3.3 2.9 + - - +
343E HIS* 3.3 36.7 + - + -
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Residues in contact with ASN 340 (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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325A PRO* 3.6 44.5 + - + +
326A GLY* 3.9 10.4 - - - +
336A GLN* 3.7 11.3 + - - +
339A ILE* 4.8 2.6 - - - +
340A ASN* 4.8 2.6 - - - +
343A HIS* 5.4 2.4 - - - -
336E GLN* 2.8 46.2 + - - +
337E GLU* 3.6 8.9 - - + +
339E ILE* 1.3 77.1 - - - +
341E ASN* 1.3 55.3 + - - +
343E HIS* 3.1 8.5 + - - +
344E LEU* 2.8 36.5 + - - +
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Residues in contact with ASN 341 (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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337E GLU* 2.7 50.4 + - - +
338E TYR* 3.5 6.5 - - + +
340E ASN* 1.3 72.3 - - - +
342E ILE* 1.3 61.8 + - + +
344E LEU* 3.9 19.2 - - - +
345E THR* 2.8 33.0 + - + +
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Residues in contact with ILE 342 (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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318E GLU* 3.7 47.3 - - + +
321E ALA* 4.1 11.0 - - + -
322E LYS* 4.3 12.1 - - + +
338E TYR* 2.9 54.0 + - + +
339E ILE 3.6 7.2 - - - +
340E ASN 3.3 0.2 - - - -
341E ASN* 1.3 76.1 - - + +
343E HIS* 1.3 63.6 + - + +
345E THR* 2.4 24.0 + - - +
346E HIS 3.9 2.8 + - - -
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Residues in contact with HIS 343 (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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340A ASN* 5.6 0.9 - - - -
343A HIS* 3.7 62.9 + + + +
347A SER* 4.6 1.8 + - - -
321E ALA 3.3 20.9 + - - -
322E LYS* 3.2 37.3 + - + +
325E PRO* 4.0 11.4 - - + +
339E ILE* 3.3 29.1 + - + -
340E ASN* 3.1 9.0 + - - +
342E ILE* 1.3 79.5 - - + +
344E LEU* 1.3 59.1 + - - +
346E HIS* 2.9 26.6 + - - +
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Residues in contact with LEU 344 (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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322A LYS 4.1 10.5 - - - +
323A TRP* 3.1 43.7 - - + +
325A PRO* 4.3 14.1 - - + +
340E ASN 2.8 20.4 + - - +
341E ASN* 3.9 19.1 - - - +
342E ILE 3.4 0.2 - - - -
343E HIS* 1.3 67.7 - - - +
345E THR* 1.3 74.4 + - + +
346E HIS* 2.9 6.9 + - - +
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Residues in contact with THR 345 (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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323A TRP* 5.8 0.5 - - - -
341E ASN* 2.8 17.9 + - + +
342E ILE* 2.4 33.3 + - - +
344E LEU* 1.3 80.0 - - + +
346E HIS* 1.3 73.0 + - - +
347E SER* 3.1 6.2 + - - +
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Residues in contact with HIS 346 (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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322A LYS* 3.3 38.3 + - + +
323A TRP* 4.6 15.9 - + + -
346A HIS* 5.2 16.0 - + + +
342E ILE 3.9 1.8 + - - -
343E HIS 2.9 20.5 + - - +
344E LEU* 2.9 6.4 - - - +
345E THR* 1.3 85.4 + - - +
347E SER* 1.4 91.1 + - - -
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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