Contacts of the helix formed by residues 332 - 348 (chain A) in PDB entry 5DO7
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 SER 332 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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283A PHE* 3.8 22.3 - - - -
286A ASP* 4.6 3.7 + - - -
328A ALA 3.4 6.6 + - - -
329A TYR* 3.5 31.5 + - - -
331A LYS* 1.3 83.1 - - - +
333A ALA* 1.3 76.7 + - - +
334A ILE* 3.2 11.2 + - - +
335A CYS* 2.8 14.4 + - - -
336A HIS* 2.9 10.3 + - - -
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Residues in contact with ALA 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A PHE* 5.1 9.9 - - + -
332A SER* 1.3 74.3 + - - +
334A ILE* 1.3 52.0 + - - +
336A HIS* 2.8 13.1 + - - +
337A LYS* 2.7 33.7 + - - +
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Residues in contact with ILE 334 (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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273A PHE* 4.5 16.8 - - + -
274A CYS 4.1 17.0 - - - +
275A GLY* 4.9 0.4 - - - -
279A GLU* 2.9 50.9 - - + +
283A PHE* 4.6 19.6 - - + -
329A TYR* 4.6 4.3 - - + -
332A SER* 3.6 15.3 + - - +
333A ALA* 1.3 78.3 - - - +
335A CYS* 1.3 77.8 - - - +
337A LYS* 2.8 19.8 + - + +
338A THR* 2.8 34.2 + - - -
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Residues in contact with CYS 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A LEU* 6.3 2.2 - - - -
272A ILE 5.0 7.4 - - - -
273A PHE* 5.9 0.7 - - - -
274A CYS* 5.7 7.4 - - - -
329A TYR* 2.4 49.1 - - - +
330A LYS* 4.2 13.2 - - - +
332A SER 2.8 9.6 + - - +
334A ILE* 1.3 79.0 - - - +
336A HIS* 1.3 68.3 + - - +
338A THR* 3.7 12.5 - - + +
339A LEU* 3.5 18.4 + - - +
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Residues in contact with HIS 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A LYS 4.7 4.6 + - - +
332A SER 2.9 9.6 + - - +
333A ALA* 2.8 14.6 + - - +
335A CYS* 1.3 74.8 - - - +
337A LYS* 1.3 65.9 + - - +
339A LEU* 2.8 32.4 + - + +
340A LYS* 2.9 49.3 + - + -
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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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262A LYS* 5.8 7.4 - - - +
279A GLU* 3.4 26.9 + - - -
333A ALA 2.7 16.4 + - - +
334A ILE* 2.8 20.9 + - + +
336A HIS* 1.3 71.2 - - - +
338A THR* 1.3 75.6 + - - +
340A LYS* 2.8 19.8 + - + +
341A ASN* 2.8 34.1 + - - +
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Residues in contact with THR 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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73A SER* 4.8 15.0 - - - +
74A LEU* 5.4 2.0 - - - -
75A TYR* 3.9 15.1 + - - +
262A LYS* 2.8 30.2 + - - +
274A CYS* 4.5 12.3 - - + +
334A ILE* 2.8 20.7 + - + +
335A CYS* 3.7 20.6 - - + +
337A LYS* 1.3 77.9 - - - +
339A LEU* 1.3 77.5 + - + +
341A ASN* 2.8 21.1 + - - +
342A ILE* 3.2 9.0 + - - +
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Residues in contact with LEU 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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41A LEU* 3.8 29.4 - - + -
42A HIS* 4.4 13.5 - - + +
73A SER* 5.2 11.2 - - - -
335A CYS 3.5 10.8 - - - +
336A HIS* 2.8 36.1 + - + +
338A THR* 1.3 78.4 - - + +
340A LYS* 1.3 66.3 + - + +
342A ILE* 2.7 32.8 + - - +
343A GLU* 2.8 27.7 + - + +
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Residues in contact with LYS 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A HIS* 2.9 52.1 + - + +
337A LYS* 2.8 16.9 + - - +
339A LEU* 1.3 74.5 - - + +
341A ASN* 1.3 53.9 + - - +
343A GLU* 2.9 16.7 + - + +
344A ARG* 2.6 35.5 + - - +
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Residues in contact with ASN 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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75A TYR* 3.3 47.6 - - + -
77A GLU* 5.5 0.6 + - - -
337A LYS* 2.8 42.7 - - - +
338A THR* 2.8 10.2 + - - +
340A LYS* 1.3 80.0 - - - +
342A ILE* 1.3 56.2 + - - +
344A ARG* 2.8 30.5 + - + +
345A MET* 3.2 6.6 + - - +
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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
----------------------------------------------------------
39A GLY* 3.6 18.6 - - - -
40A ILE 3.9 11.0 - - - +
41A LEU* 3.5 43.7 - - + -
73A SER* 5.7 0.2 - - - -
74A LEU 3.5 27.1 - - - +
75A TYR* 3.7 19.5 - - + -
114A TYR* 4.7 23.0 - - + +
338A THR 3.2 4.6 + - - +
339A LEU* 2.7 29.7 + - - +
341A ASN* 1.3 75.9 - - - +
343A GLU* 1.3 67.1 + - + +
345A MET* 3.8 10.1 + - - +
346A LYS* 4.2 9.9 + - - +
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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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41A LEU* 5.7 6.7 - - + +
339A LEU* 2.8 38.7 + - + +
340A LYS* 3.2 16.2 - - + +
342A ILE* 1.3 86.2 - - + +
344A ARG* 1.3 60.6 + - - +
345A MET 3.4 0.2 - - - -
346A LYS* 2.6 54.7 + - - +
347A HIS* 3.3 11.5 - - - +
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Residues in contact with ARG 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 LYS 2.6 15.4 + - - +
341A ASN* 2.8 21.4 + - + +
343A GLU* 1.3 74.0 - - - +
345A MET* 1.3 70.9 + - + +
347A HIS* 2.8 36.2 + - - +
348A LEU* 2.6 57.3 + - + +
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Residues in contact with MET 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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35A PRO* 5.7 4.7 - - - +
36A HIS 5.8 0.2 - - - -
37A SER* 3.6 36.6 - - - +
75A TYR* 3.4 38.6 - - + +
77A GLU* 5.1 4.9 - - - +
114A TYR* 6.1 2.9 - - + -
117A GLY* 4.6 12.9 + - - +
341A ASN 3.2 2.4 + - - +
342A ILE* 3.8 6.2 + - - +
343A GLU 3.4 0.4 - - - -
344A ARG* 1.3 101.2 - - + +
346A LYS* 1.3 54.0 + - - +
348A LEU* 2.4 44.0 - - + +
350A THR* 4.6 17.9 - - + +
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Residues in contact with LYS 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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41A LEU* 6.3 1.0 - - - +
114A TYR* 5.0 30.6 + - + +
117A GLY* 4.9 10.5 - - - -
118A ARG 5.4 4.0 - - - +
342A ILE* 4.2 5.6 + - - +
343A GLU* 2.6 55.6 + - - +
345A MET* 1.3 76.8 - - - +
347A HIS* 1.3 78.0 + - - +
348A LEU 3.0 7.8 - - - +
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Residues in contact with HIS 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A GLU 3.3 16.4 - - - +
344A ARG* 2.8 47.9 + - - +
346A LYS* 1.3 80.8 - - + +
348A LEU* 1.3 67.0 + - + +
349A LYS 4.0 0.5 + - - -
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Residues in contact with LEU 348 (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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344A ARG* 2.6 38.3 + - + +
345A MET* 2.4 41.8 - - + +
346A LYS 3.0 8.1 - - - +
347A HIS* 1.3 82.8 - - + +
349A LYS* 1.3 84.8 + - - +
350A THR* 3.8 23.8 - - + -
353A MET* 5.7 0.3 - - - +
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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