Contacts of the helix formed by residues 344 - 366 (chain B) 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 344 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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342B ALA 3.3 1.5 + - - +
343B GLN* 1.3 80.8 - - - +
345B LEU* 1.3 59.9 + - - +
346B ALA* 3.1 14.6 + - - +
347B ALA* 2.8 29.0 + - - +
348B LEU* 3.3 7.5 + - - +
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Residues in contact with LEU 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343B GLN 3.6 3.2 + - - -
344B SER* 1.3 69.2 + - - +
346B ALA* 1.3 74.6 + - - +
348B LEU* 2.8 31.1 + - + +
349B PHE* 3.3 34.3 + - + -
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Residues in contact with ALA 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B SER* 4.0 14.3 + - - +
345B LEU* 1.3 88.8 - - - +
347B ALA* 1.3 63.3 + - - +
349B PHE* 3.4 14.4 + - - +
350B LEU* 3.6 7.8 + - - +
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Residues in contact with ALA 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B ALA* 3.5 15.7 - - - +
343B GLN* 5.5 0.4 - - + -
344B SER* 2.8 22.0 + - - +
346B ALA* 1.3 77.5 - - - +
348B LEU* 1.3 54.7 + - - +
350B LEU* 2.8 19.5 + - + +
351B GLU* 2.8 28.4 + - - +
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Residues in contact with LEU 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B ALA* 4.1 28.4 + - + -
344B SER 3.3 4.4 + - - -
345B LEU* 2.8 30.2 + - + +
347B ALA* 1.3 70.3 - - - +
349B PHE* 1.3 79.1 + - + +
351B GLU* 3.3 11.6 + - - +
352B LYS* 3.0 22.9 + - + +
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Residues in contact with PHE 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345B LEU* 3.3 40.9 + - + -
346B ALA* 3.8 7.9 - - - +
347B ALA 3.2 0.6 - - - -
348B LEU* 1.3 89.0 - - + +
350B LEU* 1.3 57.4 + - - +
352B LYS* 2.8 13.2 + - + +
353B VAL* 2.8 27.7 + - - +
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Residues in contact with LEU 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B ALA 3.6 3.8 + - - +
347B ALA* 2.8 25.5 + - + +
349B PHE* 1.3 74.1 - - - +
351B GLU* 1.3 63.5 + - - +
353B VAL* 3.0 19.7 - - + +
354B ARG* 2.8 34.7 + - + +
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Residues in contact with GLU 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B ALA* 3.8 32.2 + - + +
347B ALA 2.8 14.5 + - - +
348B LEU* 3.3 16.0 - - - +
350B LEU* 1.3 75.7 - - - +
352B LYS* 1.3 66.9 + - - +
354B ARG* 3.4 5.0 + - - +
355B ASP* 3.3 17.2 + - - +
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Residues in contact with LYS 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B LEU* 3.0 14.6 + - + +
349B PHE* 2.8 15.7 + - + +
351B GLU* 1.3 75.3 - - - +
353B VAL* 1.3 60.4 + - - +
355B ASP* 2.9 26.1 + - + +
356B LEU* 2.8 29.0 + - + +
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Residues in contact with VAL 353 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349B PHE 2.8 11.4 + - - +
350B LEU* 3.0 34.1 + - + +
352B LYS* 1.3 77.2 - - - +
354B ARG* 1.3 69.4 + - - +
356B LEU* 2.8 36.3 + - + +
357B ASP* 2.8 24.2 + - - +
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Residues in contact with ARG 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B TYR* 5.6 4.6 + - - -
92B SER* 5.5 8.9 + - - -
350B LEU* 2.8 28.7 + - + +
351B GLU* 3.9 5.8 + - - +
353B VAL* 1.3 73.6 - - - +
355B ASP* 1.3 56.8 + - - +
357B ASP* 3.1 13.2 - - + +
358B ASP* 2.5 58.4 + - + +
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Residues in contact with ASP 355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351B GLU 3.3 9.6 + - - +
352B LYS* 2.9 30.6 + - + +
354B ARG* 1.3 83.1 - - - +
356B LEU* 1.3 60.0 + - - +
358B ASP* 2.8 25.2 + - - +
359B PHE* 2.8 17.2 + - - +
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Residues in contact with LEU 356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352B LYS* 2.8 17.9 + - + +
353B VAL* 2.8 34.0 + - + +
355B ASP* 1.3 72.2 + - - +
357B ASP* 1.3 66.5 + - - +
359B PHE* 3.4 7.9 + - + +
360B LEU* 3.3 29.9 + - + +
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Residues in contact with ASP 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353B VAL* 2.8 22.8 + - - +
354B ARG* 3.1 18.8 - - + +
356B LEU* 1.3 71.6 - - - +
358B ASP* 1.3 56.2 + - - +
360B LEU* 2.6 46.0 + - - +
361B TRP* 3.0 6.4 + - - +
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Residues in contact with ASP 358 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B TYR* 2.9 37.0 + - - -
354B ARG* 2.5 37.9 + - + +
355B ASP* 2.8 17.7 + - - +
357B ASP* 1.3 71.0 - - - +
359B PHE* 1.3 68.7 + - - +
361B TRP* 2.8 26.0 + - - +
362B LYS* 3.4 3.6 + - - +
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Residues in contact with PHE 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355B ASP* 2.8 16.1 + - - +
356B LEU* 3.8 10.8 - - + +
357B ASP 3.3 0.2 - - - -
358B ASP* 1.3 77.0 + - - +
360B LEU* 1.3 57.1 + - + +
362B LYS* 3.0 35.3 + - + +
363B ALA* 2.8 48.6 + - + -
366B LYS* 5.7 4.7 - - + -
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Residues in contact with LEU 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356B LEU* 3.3 28.9 + - + +
357B ASP* 2.6 28.1 + - - +
359B PHE* 1.3 77.1 - - + +
361B TRP* 1.3 60.9 + - - +
363B ALA* 2.8 23.0 + - + +
364B GLU* 2.8 17.7 + - - +
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Residues in contact with TRP 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B SER* 5.0 4.4 - - - -
36B LEU 4.0 9.2 + - - +
37B TYR* 3.3 36.5 - + + +
93B PHE 4.9 2.8 + - - -
94B LYS* 3.9 34.3 - - + -
95B VAL 3.5 36.3 + - - -
96B ARG* 3.6 46.4 + - + +
99B GLN* 4.4 1.8 - - - -
135B ASN 5.7 3.6 + - - -
357B ASP 3.0 6.8 + - - +
358B ASP* 2.8 25.4 + - - +
360B LEU* 1.3 73.2 - - - +
362B LYS* 1.3 59.1 + - - +
364B GLU* 3.7 6.3 + - - +
365B THR* 3.7 15.8 + - - -
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Residues in contact with LYS 362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B TYR* 4.7 17.5 - - + +
135B ASN 4.9 3.6 - - - +
136B GLY* 4.5 25.1 - - - -
358B ASP 3.4 2.6 + - - +
359B PHE* 3.0 34.7 + - + +
361B TRP* 1.3 81.4 - - + +
363B ALA* 1.3 54.3 + - - +
365B THR* 2.8 13.2 + - - -
366B LYS* 2.8 68.9 + - + +
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Residues in contact with ALA 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359B PHE* 2.8 36.7 + - + +
360B LEU* 2.8 30.4 + - + +
362B LYS* 1.3 72.0 - - - +
364B GLU* 1.3 61.7 + - - +
366B LYS* 3.2 26.7 + - - +
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Residues in contact with GLU 364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B ARG* 3.4 32.5 - - - +
360B LEU* 2.8 17.4 + - - +
361B TRP* 3.9 5.8 - - - +
363B ALA* 1.3 74.3 - - - +
365B THR* 1.3 63.5 + - - +
366B LYS 3.3 5.4 + - - +
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Residues in contact with THR 365 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B ASP* 5.1 17.6 + - - +
34B ASN 5.9 0.2 - - - -
35B SER* 5.3 7.3 + - - -
96B ARG* 5.1 5.6 + - - +
135B ASN* 3.3 47.6 + - + +
136B GLY* 4.2 6.7 - - - +
361B TRP* 3.7 9.2 + - - -
362B LYS* 2.8 19.4 + - + +
364B GLU* 1.3 76.8 - - - +
366B LYS* 1.3 61.4 + - + +
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Residues in contact with LYS 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359B PHE* 5.7 4.7 - - + -
362B LYS* 2.8 49.1 + - + +
363B ALA* 3.2 19.5 + - - +
364B GLU 3.8 4.2 - - - +
365B THR* 1.3 81.9 - - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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