Contacts of the helix formed by residues 336 - 351 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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332B TYR* 2.9 28.6 + - - +
333B LEU 3.5 7.5 - - - +
334B VAL 3.3 0.2 - - - -
335B MET* 1.3 92.3 + - - +
337B PRO* 1.3 61.9 - - - +
338B ARG* 3.0 8.7 + - + +
339B VAL* 2.8 36.8 + - + +
340B GLN 3.3 6.4 + - - -
427B PHE* 3.9 31.5 - - + +
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Residues in contact with PRO 337 (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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333B LEU 3.6 8.0 - - - +
334B VAL* 3.6 12.8 - - - +
335B MET 3.5 7.2 - - - +
336B ASN* 1.3 87.4 - - - +
338B ARG* 1.3 62.4 + - - +
340B GLN* 3.2 18.8 + - + +
341B ARG* 3.2 26.9 + - + +
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Residues in contact with ARG 338 (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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336B ASN* 3.0 7.0 + - - +
337B PRO* 1.3 80.4 - - - +
339B VAL* 1.3 82.8 + - + +
341B ARG* 3.5 30.4 + - - +
342B LYS* 3.4 31.1 + - + +
367B TYR* 4.3 3.2 + - - -
427B PHE 4.5 4.6 + - - -
428B LEU* 4.2 15.6 - - - +
429B PRO* 4.4 3.0 - - - +
430B GLU* 2.7 38.6 + - - -
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Residues in contact with VAL 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332B TYR 5.7 0.7 - - - +
333B LEU* 4.8 1.3 - - + -
336B ASN* 2.8 27.9 + - + +
338B ARG* 1.3 96.3 - - - +
340B GLN* 1.3 64.6 + - - +
342B LYS 3.5 0.5 + - - -
343B ILE* 3.2 24.6 + - + +
367B TYR* 3.4 32.4 - - + +
371B PHE* 3.7 33.0 - - + -
427B PHE* 4.4 4.0 - - + -
429B PRO* 4.0 16.2 - - + -
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Residues in contact with GLN 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B LEU* 3.3 48.5 + - + +
336B ASN 3.3 3.2 + - - -
337B PRO* 3.2 14.5 + - - +
339B VAL* 1.3 79.8 - - - +
341B ARG* 1.3 62.0 + - + +
343B ILE* 3.4 4.4 + - - +
344B GLN* 3.1 44.5 + - - +
475B LEU* 3.8 16.5 - - + +
479B GLU* 3.6 4.3 - - - -
480B PHE* 2.9 46.9 + - - +
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Residues in contact with ARG 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337B PRO* 3.2 17.4 + - + +
338B ARG* 3.6 42.6 + - - +
340B GLN* 1.3 75.5 - - + +
342B LYS* 1.3 58.3 + - + +
344B GLN* 2.9 16.2 + - - +
345B GLU* 2.5 58.7 + - + +
479B GLU* 5.8 2.5 - - - +
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Residues in contact with LYS 342 (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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338B ARG* 3.4 24.2 + - + +
339B VAL 3.9 2.5 - - - +
340B GLN 3.4 0.4 - - - -
341B ARG* 1.3 80.2 - - + +
343B ILE* 1.3 57.8 + - - +
345B GLU* 3.9 17.4 - - - +
346B GLU* 3.0 28.8 + - - +
367B TYR* 3.5 44.2 - - + +
430B GLU* 3.3 28.8 + - - +
433B LEU* 5.3 2.2 - - - +
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Residues in contact with ILE 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B LEU* 3.6 27.6 - - + -
339B VAL* 3.2 19.0 + - + +
340B GLN* 3.6 6.1 - - - +
341B ARG 3.1 0.4 - - - -
342B LYS* 1.3 75.5 - - - +
344B GLN* 1.3 58.2 + - - +
346B GLU* 3.2 7.9 + - - +
347B LEU* 2.9 38.8 + - + +
367B TYR* 3.6 20.0 - - + +
368B MET* 4.1 23.8 - - + -
371B PHE* 3.7 28.7 - - + -
475B LEU* 3.5 24.7 - - + -
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Residues in contact with GLN 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340B GLN* 3.1 36.5 + - - +
341B ARG* 2.9 17.2 + - - +
343B ILE* 1.3 75.7 - - - +
345B GLU* 1.3 63.0 + - + +
347B LEU* 3.3 7.9 + - - +
348B ASP* 3.0 31.4 + - - +
475B LEU* 3.5 24.6 + - + +
478B VAL 3.6 11.5 + - - -
479B GLU* 3.4 36.7 - - - +
511B ARG* 3.4 26.8 + - - +
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Residues in contact with GLU 345 (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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341B ARG* 2.5 45.8 + - + +
342B LYS* 3.9 17.2 - - - +
344B GLN* 1.3 72.8 - - + +
346B GLU* 1.3 62.2 + - - +
348B ASP* 3.4 7.5 + - - +
349B THR* 3.1 27.8 + - - -
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Residues in contact with GLU 346 (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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342B LYS 3.0 19.1 + - - +
343B ILE* 3.2 5.2 + - - +
345B GLU* 1.3 73.9 - - - +
347B LEU* 1.3 64.5 + - - +
349B THR* 3.4 4.4 + - - +
350B VAL* 3.1 32.5 + - + +
365B LEU* 3.6 25.5 - - + +
366B PRO* 3.0 17.8 - - - +
367B TYR* 2.9 29.8 + - + +
368B MET* 3.1 26.3 + - - +
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Residues in contact with LEU 347 (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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343B ILE* 2.9 29.4 + - + +
344B GLN* 3.3 9.2 + - - +
346B GLU* 1.3 76.9 - - - +
348B ASP* 1.3 60.9 + - - +
351B ILE* 3.0 42.0 + - + +
352B GLY 3.2 6.2 + - - +
357B PRO* 4.6 2.9 - - + -
365B LEU* 3.7 31.6 - - + -
368B MET* 5.5 3.1 - - + -
472B ALA* 3.9 23.1 - - + +
475B LEU* 4.0 13.0 - - + -
476B GLN* 3.6 41.3 - - + +
511B ARG* 5.2 0.2 - - - +
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Residues in contact with ASP 348 (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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344B GLN 3.0 13.1 + - - +
345B GLU* 3.8 6.9 - - - +
346B GLU 3.3 0.2 - - - -
347B LEU* 1.3 77.9 - - - +
349B THR* 1.3 63.6 + - - +
351B ILE 4.1 0.2 - - - -
352B GLY* 3.1 26.5 + - - +
353B ARG* 3.7 19.6 + - + -
476B GLN* 5.2 1.0 - - - +
511B ARG* 2.8 39.8 + - - -
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Residues in contact with THR 349 (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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345B GLU 3.1 17.1 + - - -
346B GLU* 3.9 5.8 - - - -
347B LEU 3.3 0.2 - - - -
348B ASP* 1.3 79.0 - - - +
350B VAL* 1.3 68.9 + - + +
351B ILE 3.8 0.3 + - - -
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Residues in contact with VAL 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B GLU* 3.1 25.9 + - + +
349B THR* 1.3 87.4 - - + +
351B ILE* 1.3 64.5 + - + +
355B ARG* 5.0 3.3 + - - -
361B ASP* 5.6 3.6 - - + +
364B HIS* 3.6 39.9 - - + +
365B LEU* 3.8 14.8 - - + -
366B PRO* 5.9 0.4 - - + -
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Residues in contact with ILE 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347B LEU* 3.0 17.5 + - + +
348B ASP 4.1 0.2 - - - -
349B THR 3.5 0.6 - - - -
350B VAL* 1.3 94.5 - - + +
352B GLY* 1.3 70.0 + - - +
354B SER* 3.9 11.4 + - - -
355B ARG* 3.9 45.3 + - + +
357B PRO* 3.9 24.5 - - + -
361B ASP* 3.7 23.1 - - - +
365B LEU* 4.1 21.8 - - + -
476B GLN* 4.5 3.8 - - - +
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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