Contacts of the helix formed by residues 339 - 348 (chain D) in PDB entry 4O9U
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 339 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28C VAL 5.7 0.7 - - - -
31C HIS* 5.6 3.1 - - - +
32C THR* 3.2 13.9 + - - -
332D PRO* 4.0 13.5 + - - -
337D MET 3.4 2.0 + - - -
338D PRO* 1.3 71.8 - - - +
340D HIS* 1.3 63.4 + - - +
341D MET 3.2 2.0 - - - -
342D ASN* 3.3 33.2 + - - +
343D VAL* 3.3 18.2 + - - +
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Residues in contact with HIS 340 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79D THR* 3.2 32.2 + - - -
82D PRO* 5.7 1.8 - - + -
301D TYR* 5.1 4.3 - + - -
304D ALA* 4.0 18.3 - - + +
334D ALA 3.6 17.9 + - - +
335D GLY* 4.1 3.6 - - - -
336D ARG* 3.1 35.5 + - + -
337D MET* 3.5 38.0 + - + +
338D PRO 3.3 1.8 - - - -
339D GLY* 1.3 76.2 - - - +
341D MET* 1.3 66.2 + - + +
343D VAL* 3.8 2.3 - - + +
344D LEU* 3.5 33.5 + - + +
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Residues in contact with MET 341 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299D PRO* 3.4 44.4 - - + +
300D GLY 3.4 22.9 - - - +
301D TYR* 5.1 0.7 - - - -
303D MET* 3.8 13.5 - - + -
304D ALA* 5.3 1.3 - - + -
330D ILE* 4.0 20.2 - - + -
331D HIS 4.7 1.3 - - - +
334D ALA* 3.3 38.8 - - + +
335D GLY* 4.5 1.8 - - - -
339D GLY* 3.2 0.4 - - - -
340D HIS* 1.3 89.3 - - + +
342D ASN* 1.3 56.8 + - - +
344D LEU* 4.9 2.5 - - + -
345D LEU* 2.8 54.9 + - + +
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Residues in contact with ASN 342 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C VAL* 3.1 30.9 + - - +
29C ILE* 3.2 29.8 + - - +
32C THR* 4.6 4.0 + - - +
33C PRO* 5.7 1.1 - - + -
330D ILE* 3.5 22.9 - - - +
332D PRO* 6.0 0.5 - - - +
339D GLY* 3.3 28.5 + - - +
341D MET* 1.3 75.8 - - - +
343D VAL* 1.3 61.9 + - + +
345D LEU* 3.5 2.4 - - - +
346D ALA* 2.9 28.0 + - - +
352D TYR* 4.2 10.2 - - + +
355D LEU* 4.2 13.0 - - + -
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Residues in contact with VAL 343 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C THR* 4.2 8.1 - - - -
33C PRO* 4.7 3.1 - - + -
86C MET* 3.4 35.9 - - + -
78D MET* 3.9 34.3 - - + +
79D THR* 5.1 2.9 - - - -
337D MET* 3.4 28.7 - - + -
339D GLY 3.3 11.6 + - - +
340D HIS 3.8 4.3 - - - +
342D ASN* 1.3 76.4 - - + +
344D LEU* 1.3 63.7 - - + +
346D ALA* 3.4 8.3 - - + +
347D GLU* 2.8 27.0 + - - +
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Residues in contact with LEU 344 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78D MET* 5.7 0.4 - - + -
79D THR* 4.5 17.3 - - - +
303D MET* 3.8 25.6 - - + -
304D ALA* 4.0 23.8 - - + -
307D GLN* 4.2 11.2 - - - +
309D GLN* 3.4 44.4 - - + +
340D HIS* 3.5 23.1 + - + +
341D MET 4.1 1.8 - - - +
342D ASN 3.3 0.2 - - - -
343D VAL* 1.3 79.6 - - + +
345D LEU* 1.3 56.9 + - - +
346D ALA 2.9 4.5 - - - -
347D GLU* 3.8 19.2 - - + +
348D ALA* 3.0 30.8 + - - +
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Residues in contact with LEU 345 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299D PRO* 4.2 8.5 - - + -
303D MET* 4.9 7.9 - - + -
309D GLN* 6.0 3.6 - - + +
312D LEU* 4.3 14.6 - - + -
328D PHE* 3.9 22.7 - - + -
330D ILE* 3.3 34.3 - - + -
341D MET* 2.8 36.3 + - + +
342D ASN 3.5 2.0 - - - -
344D LEU* 1.3 70.4 - - - +
346D ALA* 1.3 55.7 + - - +
348D ALA* 4.9 1.1 - - + -
349D GLY 4.4 0.7 - - - -
350D VAL* 3.1 53.9 + - + +
352D TYR* 5.0 1.3 - - - -
355D LEU* 3.7 24.4 - - + +
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Residues in contact with ALA 346 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89C MET* 3.6 29.9 - - + +
78D MET* 5.4 0.2 - - + -
342D ASN 2.9 17.6 + - - +
343D VAL* 3.4 13.2 - - + +
344D LEU 2.9 0.2 - - - -
345D LEU* 1.3 77.3 - - - +
347D GLU* 1.3 63.8 + - - +
348D ALA 3.2 1.8 - - - -
349D GLY* 3.2 15.3 + - - -
350D VAL 5.1 1.1 - - - -
352D TYR* 3.4 26.7 - - + +
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Residues in contact with GLU 347 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89C MET* 4.2 14.1 - - + +
77D ALA* 5.4 1.9 - - - +
78D MET* 3.1 44.4 + - + +
79D THR* 4.5 2.6 + - - +
307D GLN* 5.2 3.0 - - - +
309D GLN* 5.1 1.4 + - - -
310D HIS* 3.4 30.9 + - + -
343D VAL 2.8 20.1 + - - +
344D LEU* 3.2 21.6 + - + +
346D ALA* 1.3 73.6 - - - +
348D ALA* 1.3 61.6 + - - +
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Residues in contact with ALA 348 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309D GLN* 4.2 22.2 - - + +
310D HIS* 4.1 24.9 + - + +
313D LYS* 4.7 16.6 - - + +
344D LEU 3.0 15.8 + - - +
345D LEU* 4.9 0.7 - - + -
347D GLU* 1.3 79.8 - - - +
349D GLY* 1.3 58.7 + - - +
350D VAL* 4.7 6.5 - - + -
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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