Contacts of the helix formed by residues 326 - 341 (chain B) in PDB entry 3DDN
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 PRO 326 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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322B GLU 3.2 21.3 - - - +
323B GLU* 3.7 6.7 - - - +
324B VAL 3.3 4.5 - - - -
325B ALA* 1.3 91.6 - - + +
327B TRP* 1.3 57.8 + - - +
328B LEU 3.4 0.4 + - - -
329B ASP* 4.2 6.9 + - - +
330B LEU 4.4 3.6 + - - -
431B LEU* 3.5 32.9 - - + +
436B LEU* 4.0 24.2 - - + -
438B GLN* 4.5 7.8 + - - +
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Residues in contact with TRP 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B GLU 3.2 27.2 + - - -
324B VAL 2.9 10.5 + - - +
326B PRO* 1.3 73.8 - - + +
328B LEU* 1.3 66.7 + - - +
329B ASP 3.2 2.2 - - - -
330B LEU* 3.3 21.6 + - + +
331B VAL* 2.8 27.3 + - + +
357B LEU* 3.7 22.0 - - + +
365B LEU* 4.0 17.9 - - + -
411B SER* 3.9 29.6 - - - -
413B VAL* 3.7 26.0 - - + -
429B GLY 3.7 20.2 - - - -
430B THR* 3.8 15.7 - - - -
431B LEU* 3.5 44.1 - - + +
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Residues in contact with LEU 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B PHE* 4.0 11.4 - - + -
310B PRO* 3.8 34.3 - - + -
320B VAL* 4.2 4.9 - - + -
324B VAL 3.7 3.1 + - - +
325B ALA* 3.2 25.2 + - - +
327B TRP* 1.3 77.3 - - - +
329B ASP* 1.3 57.1 + - + +
331B VAL 3.3 0.2 + - - -
332B ARG* 3.1 25.1 + - - +
364B VAL* 3.6 37.0 - - + -
365B LEU* 4.0 6.0 - - + +
368B SER* 3.2 31.6 - - - +
384B PHE* 4.4 6.3 - - + -
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Residues in contact with ASP 329 (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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325B ALA 4.7 0.8 + - - +
326B PRO 4.2 4.2 + - - +
327B TRP 3.2 0.6 - - - -
328B LEU* 1.3 77.4 - - + +
330B LEU* 1.3 64.4 + - - +
332B ARG* 2.8 40.3 + - - +
333B LYS* 3.0 39.2 + - - +
438B GLN* 3.1 24.2 + - - +
529B SER 4.5 3.0 - - - +
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Residues in contact with LEU 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326B PRO 4.4 0.6 + - - -
327B TRP* 3.5 36.9 - - + +
329B ASP* 1.3 78.9 - - - +
331B VAL* 1.3 58.9 + - - +
333B LYS* 3.0 6.6 + - + +
334B LEU* 2.9 44.4 + - + +
429B GLY* 3.7 5.2 - - - -
430B THR 3.7 26.7 - - - +
431B LEU* 4.0 11.0 - - + -
438B GLN* 3.9 33.4 + - + +
439B LYS 4.2 13.7 - - - +
440B ILE* 5.3 0.7 - - + +
452B ALA* 4.3 12.3 - - + -
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Residues in contact with VAL 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B TRP* 2.8 29.2 + - + +
328B LEU 4.0 2.7 - - - +
330B LEU* 1.3 75.1 - - + +
332B ARG* 1.3 62.4 + - - +
334B LEU* 3.3 10.6 + - + +
335B GLY 3.1 16.6 + - - -
351B VAL* 4.4 5.2 - - + -
365B LEU* 3.3 44.0 - - + +
368B SER* 4.4 2.2 - - - -
369B ALA* 3.7 17.4 - - + +
413B VAL* 4.0 31.2 - - + -
415B VAL* 4.4 11.0 - - + -
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Residues in contact with ARG 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B LEU 3.1 13.7 + - - +
329B ASP* 2.8 42.2 + - - +
331B VAL* 1.3 75.9 - - - +
333B LYS* 1.3 82.6 + - - +
335B GLY 3.0 2.9 + - - -
336B VAL* 2.9 47.9 + - - +
368B SER* 3.5 23.0 - - - +
371B ARG* 4.2 30.0 - - + +
372B GLY* 3.4 14.7 - - - +
375B SER* 5.6 1.4 + - - -
527B ASP 5.2 6.5 + - - -
528B LEU* 5.3 1.4 - - - +
529B SER 4.3 15.8 + - - -
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Residues in contact with LYS 333 (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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329B ASP* 3.2 26.5 + - - +
330B LEU* 3.0 9.2 + - + +
332B ARG* 1.3 91.5 - - - +
334B LEU* 1.3 58.3 + - + +
336B VAL* 3.2 10.6 + - - +
337B LEU* 2.9 36.0 + - + +
438B GLN* 2.9 26.0 + - - +
440B ILE* 6.3 0.2 - - + -
452B ALA* 2.8 36.0 + - + +
453B GLN* 4.7 1.8 - - - +
528B LEU* 2.9 38.2 + - + +
529B SER* 3.5 15.7 + - - +
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Residues in contact with LEU 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330B LEU* 2.9 26.4 + - + +
331B VAL* 3.6 20.0 - - + +
332B ARG 3.2 0.2 - - - -
333B LYS* 1.3 76.2 - - + +
335B GLY* 1.3 57.9 + - - +
337B LEU* 3.4 10.1 + - + +
338B ALA* 2.8 30.1 + - - +
413B VAL* 3.5 33.0 - - + +
415B VAL* 3.6 24.1 - - + +
427B VAL* 3.6 26.9 - - + +
428B SER 3.7 17.3 - - - +
429B GLY* 3.7 12.1 - - - +
440B ILE* 4.9 4.7 - - + -
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Residues in contact with GLY 335 (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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331B VAL 3.1 7.8 + - - -
332B ARG 3.0 7.7 + - - -
334B LEU* 1.3 73.4 - - - +
336B VAL* 1.3 66.1 + - - +
338B ALA* 3.9 1.9 - - - +
339B GLY* 3.0 18.4 + - - -
369B ALA 3.5 21.1 - - - -
372B GLY 3.6 6.5 - - - -
373B LEU* 3.5 13.1 - - - +
415B VAL* 4.3 13.8 - - - +
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Residues in contact with VAL 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332B ARG* 2.9 35.8 + - - +
333B LYS* 3.4 13.2 - - - +
335B GLY* 1.3 77.4 - - - +
337B LEU* 1.3 63.6 + - - +
339B GLY* 3.2 1.0 + - - -
340B VAL* 3.0 25.6 + - + +
372B GLY* 3.4 24.2 + - - +
375B SER* 4.0 9.4 - - - +
376B ALA* 3.8 12.3 - - + +
526B VAL* 3.7 26.2 - - + -
527B ASP 4.7 6.3 - - - +
528B LEU* 4.7 2.0 - - + -
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Residues in contact with LEU 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 LYS* 2.9 22.8 + - + +
334B LEU* 3.5 5.8 - - + +
336B VAL* 1.3 76.8 - - - +
338B ALA* 1.3 63.1 + - - +
340B VAL* 3.4 2.4 + - - +
341B LEU* 2.9 38.9 + - + +
427B VAL* 3.8 27.4 - - + -
440B ILE* 3.9 26.5 - - + -
443B ILE* 5.1 3.8 - - + -
458B ILE* 4.7 8.7 - - + -
526B VAL* 3.6 37.2 - - + -
528B LEU* 3.8 21.1 - - + -
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Residues in contact with ALA 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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334B LEU 2.8 20.9 + - - +
335B GLY* 3.9 3.6 - - - +
337B LEU* 1.3 73.2 - - - +
339B GLY* 1.3 61.6 + - - +
341B LEU* 3.9 1.6 - - - +
342B SER* 3.1 26.3 + - - -
349B LEU* 4.8 2.9 - - + -
415B VAL* 4.0 28.5 - - + +
417B ALA* 4.1 19.5 - - + +
425B VAL* 4.3 8.6 - - + +
427B VAL* 4.1 12.3 - - + +
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Residues in contact with GLY 339 (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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335B GLY 3.0 10.5 + - - -
336B VAL 3.6 2.9 - - - -
338B ALA* 1.3 75.1 - - - +
340B VAL* 1.3 66.5 + - - +
342B SER* 3.0 25.0 + - - +
346B PRO* 5.4 2.3 - - - +
373B LEU* 3.5 29.1 - - - +
376B ALA* 4.9 5.6 - - - -
377B VAL* 5.5 6.2 - - - +
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Residues in contact with VAL 340 (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 VAL* 3.0 21.2 + - + +
337B LEU 4.1 1.3 - - - +
339B GLY* 1.3 75.5 - - - +
341B LEU* 1.3 61.4 + - + +
342B SER 3.4 6.6 + - - +
376B ALA* 3.8 21.8 - - + +
522B LYS* 3.8 1.0 + - - -
524B GLU* 3.6 40.2 - - + +
525B VAL 4.4 6.1 - - - +
526B VAL* 3.8 32.8 - - + -
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Residues in contact with LEU 341 (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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337B LEU* 2.9 28.5 + - + +
338B ALA 3.9 0.2 - - - -
340B VAL* 1.3 79.0 - - + +
342B SER* 1.3 59.8 + - - +
343B ASP* 3.6 1.6 + - - +
425B VAL* 3.8 25.8 - - + +
427B VAL* 4.2 11.9 - - + -
443B ILE* 4.2 33.4 - - + -
444B ASN* 5.9 0.2 - - - +
458B ILE* 4.3 28.3 - - + -
522B LYS* 3.1 33.8 + - + +
524B GLU* 3.9 28.5 - - + -
526B VAL* 5.3 0.9 - - + -
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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
------------------------------------------------------------
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