Contacts of the helix formed by residues 336 - 351 (chain D) in PDB entry 6DWM
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 ASN 336 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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332D TYR* 2.9 33.0 + - - +
333D LEU 3.4 7.0 - - - +
335D MET* 1.3 91.6 + - - +
337D PRO* 1.3 60.6 - - - +
338D ARG* 3.1 5.6 + - + +
339D VAL* 2.9 37.1 + - + +
340D GLN 3.4 6.4 + - - -
427D PHE* 3.8 33.4 - - + +
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Residues in contact with PRO 337 (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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333D LEU 3.6 7.8 - - - +
334D VAL* 3.5 13.7 - - - +
335D MET 3.5 7.6 - - - +
336D ASN* 1.3 88.3 - - - +
338D ARG* 1.3 61.9 + - - +
340D GLN* 3.2 17.4 + - + +
341D ARG* 3.4 31.0 + - - +
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Residues in contact with ARG 338 (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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336D ASN* 3.1 3.4 + - + -
337D PRO* 1.3 80.0 - - - +
339D VAL* 1.3 81.5 + - + +
341D ARG* 3.6 19.7 + - - +
342D LYS* 3.5 37.0 + - + +
367D TYR* 4.3 0.4 + - - -
427D PHE 4.7 4.2 + - - -
428D LEU* 4.2 12.6 - - - +
429D PRO* 4.5 2.4 - - - +
430D GLU* 2.9 39.0 + - - -
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Residues in contact with VAL 339 (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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332D TYR 5.5 0.4 - - - +
333D LEU* 4.7 1.8 - - + -
336D ASN* 2.9 28.0 + - + +
338D ARG* 1.3 101.4 - - - +
340D GLN* 1.3 63.9 + - - +
342D LYS* 3.5 0.9 + - - -
343D ILE* 3.2 23.8 + - + +
367D TYR* 3.7 26.3 - - + +
371D PHE* 3.7 33.2 - - + -
427D PHE* 4.2 4.9 - - + +
429D PRO* 4.0 17.9 - - + -
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Residues in contact with GLN 340 (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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333D LEU* 3.3 51.8 + - + +
334D VAL* 4.8 0.4 - - - +
336D ASN 3.4 2.4 + - - -
337D PRO* 3.2 13.8 + - - +
339D VAL* 1.3 80.6 - - - +
341D ARG* 1.3 62.4 + - + +
343D ILE* 3.4 4.7 + - - +
344D GLN* 3.1 42.5 + - - +
475D LEU* 3.8 14.3 - - + +
479D GLU* 3.8 3.3 - - - -
480D PHE* 2.9 46.9 + - - +
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Residues in contact with ARG 341 (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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337D PRO* 3.4 29.0 + - - +
338D ARG* 3.6 18.5 + - - +
340D GLN* 1.3 76.5 - - + +
342D LYS* 1.3 55.7 + - - +
344D GLN* 3.6 17.2 - - + +
345D GLU* 2.5 57.4 + - + +
479D GLU* 5.2 6.5 - - + +
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Residues in contact with LYS 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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338D ARG* 3.5 28.1 + - + +
339D VAL 3.8 3.4 - - - +
340D GLN 3.4 0.4 - - - -
341D ARG* 1.3 76.8 - - + +
343D ILE* 1.3 61.4 + - - +
345D GLU* 3.8 16.7 - - - +
346D GLU* 3.0 24.4 + - - +
367D TYR* 3.5 47.1 - - + +
430D GLU* 2.8 31.1 + - - +
433D LEU* 5.3 2.2 - - - +
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Residues in contact with ILE 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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333D LEU* 3.6 31.4 - - + -
339D VAL* 3.2 13.5 + - + +
340D GLN 3.6 6.7 - - - +
341D ARG 3.1 0.2 - - - -
342D LYS* 1.3 77.0 - - - +
344D GLN* 1.3 57.3 + - - +
346D GLU* 3.2 7.3 + - - +
347D LEU* 3.0 38.4 + - + +
367D TYR* 3.7 18.6 - - + -
368D MET* 3.7 42.6 - - + -
371D PHE* 3.7 15.5 - - + -
475D LEU* 3.7 21.8 - - + -
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Residues in contact with GLN 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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340D GLN* 3.1 42.3 + - - +
341D ARG* 3.0 18.4 + - - +
343D ILE* 1.3 75.7 - - - +
345D GLU* 1.3 63.3 + - + +
347D LEU* 3.3 8.3 + - - +
348D ASP* 3.0 30.7 + - - +
475D LEU* 3.4 27.4 + - + +
478D VAL 3.6 11.3 + - - -
479D GLU* 3.5 31.3 - - - +
511D ARG* 3.4 25.4 + - - +
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Residues in contact with GLU 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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341D ARG* 2.5 47.1 + - + +
342D LYS* 3.8 15.6 - - - +
344D GLN* 1.3 73.9 - - + +
346D GLU* 1.3 56.4 + - - +
348D ASP* 3.4 7.0 + - - +
349D THR* 3.0 33.9 + - - +
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Residues in contact with GLU 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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342D LYS 3.0 18.5 + - - +
343D ILE* 3.6 5.0 - - - +
345D GLU* 1.3 73.9 - - - +
347D LEU* 1.3 65.8 + - - +
349D THR* 4.6 4.3 - - - -
350D VAL* 2.9 39.9 + - + +
365D LEU* 3.7 26.5 - - + +
366D PRO* 3.1 17.7 - - - +
367D TYR* 2.9 30.1 + - + +
368D MET* 3.1 26.3 + - - +
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Residues in contact with LEU 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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343D ILE* 3.0 25.9 + - + +
344D GLN* 3.6 9.4 - - - +
346D GLU* 1.3 76.8 - - - +
348D ASP* 1.3 61.2 + - - +
351D ILE* 2.9 42.1 + - + +
352D GLY 3.2 6.0 + - - +
357D PRO* 4.5 4.7 - - + -
365D LEU* 3.9 32.3 - - + -
368D MET* 5.6 3.4 - - + -
472D ALA* 3.8 24.5 - - + +
475D LEU* 4.1 13.2 - - + -
476D GLN* 3.7 38.1 - - + +
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Residues in contact with ASP 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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344D GLN 3.0 15.8 + - - +
345D GLU* 3.8 6.2 - - - +
347D LEU* 1.3 79.1 - - - +
349D THR* 1.3 60.3 + - - +
352D GLY* 2.9 30.8 + - - +
353D ARG* 3.7 21.4 + - + +
476D GLN* 4.8 1.9 - - - +
511D ARG* 2.8 39.6 + - - -
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Residues in contact with THR 349 (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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349A THR* 5.3 6.1 + - - +
345D GLU* 3.0 18.2 + - - +
346D GLU* 3.9 5.4 - - - -
348D ASP* 1.3 79.0 - - - +
350D VAL* 1.3 69.0 + - + +
351D ILE 3.7 0.5 + - - -
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Residues in contact with VAL 350 (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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349A THR* 3.6 39.7 + - + +
346D GLU* 2.9 32.6 + - + +
349D THR* 1.3 85.8 - - + +
351D ILE* 1.3 65.3 + - + +
355D ARG* 4.9 3.8 + - - -
361D ASP* 5.6 2.5 - - + +
364D HIS* 3.7 33.7 - - + +
365D LEU* 3.9 11.9 - - + -
366D PRO* 5.9 0.2 - - + -
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Residues in contact with ILE 351 (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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347D LEU* 2.9 26.5 + - + +
348D ASP 3.9 0.2 - - - -
349D THR 3.5 0.6 - - - -
350D VAL* 1.3 91.8 - - + +
352D GLY* 1.3 70.0 + - - +
354D SER* 4.8 5.0 + - - -
355D ARG* 3.7 51.5 + - + +
357D PRO* 3.9 22.9 - - + -
361D ASP* 3.6 30.3 - - + +
365D LEU* 4.3 5.8 - - + -
476D GLN* 4.7 2.9 - - - +
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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
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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