Contacts of the helix formed by residues 362 - 376 (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 VAL 362 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324B VAL* 4.1 6.3 - - + -
353B VAL* 4.0 14.6 - - + -
357B LEU* 3.9 33.2 - - + +
360B GLU 4.1 2.0 - - - +
361B GLU* 1.3 78.5 - - - +
363B GLU* 1.3 69.3 + - - +
364B VAL 3.0 3.1 - - - +
365B LEU* 2.9 45.0 + - + +
400B ILE* 3.5 9.8 - - + +
402B LYS* 3.1 37.9 - - + -
531B TLA 3.0 4.0 + - - +
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Residues in contact with GLU 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361B GLU 3.7 0.6 - - - -
362B VAL* 1.3 70.4 - - - +
364B VAL* 1.3 65.9 + - - +
366B ARG* 2.8 60.8 + - - +
367B LEU* 3.7 5.4 + - + +
400B ILE* 3.4 27.7 - - - +
531B TLA 2.7 43.5 + - - +
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Residues in contact with VAL 364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B PHE* 4.3 12.8 - - + -
320B VAL* 4.4 14.1 - - + -
324B VAL* 4.0 22.9 - - + -
328B LEU* 3.6 23.3 - - + -
361B GLU 4.9 2.4 - - - +
362B VAL* 3.0 4.4 + - - +
363B GLU* 1.3 81.7 - - - +
365B LEU* 1.3 57.5 + - - +
367B LEU* 3.2 15.3 + - + +
368B SER* 3.0 25.9 + - - -
384B PHE* 3.3 30.3 - - + -
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Residues in contact with LEU 365 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324B VAL* 4.0 17.3 - - + -
327B TRP* 4.0 28.3 - - + +
328B LEU* 4.0 22.7 - - + +
331B VAL* 3.3 27.5 - - + +
351B VAL* 4.4 6.0 - - + +
353B VAL* 4.3 8.1 - - + -
357B LEU* 4.0 19.7 - - + -
362B VAL* 2.9 38.7 + - + +
364B VAL* 1.3 74.9 - - - +
366B ARG* 1.3 57.2 + - - +
368B SER* 4.0 2.2 - - - +
369B ALA* 3.0 24.4 + - - +
400B ILE* 4.6 5.2 - - + -
413B VAL* 4.4 0.9 - - + -
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Residues in contact with ARG 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349B LEU* 5.3 0.7 - - + +
351B VAL* 4.1 15.9 - - + +
362B VAL 3.9 0.8 + - - -
363B GLU* 2.8 29.9 + - - +
365B LEU* 1.3 74.4 - - - +
367B LEU* 1.3 96.9 + - - +
369B ALA* 3.4 2.6 + - - +
370B LEU* 3.1 28.0 + - + +
388B PRO* 5.4 6.9 - - - +
398B ALA* 4.0 31.2 + - + +
399B GLU* 4.3 2.0 - - - +
400B ILE* 3.9 41.9 - - + +
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Residues in contact with LEU 367 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363B GLU* 4.3 4.0 - - + +
364B VAL* 3.2 21.0 + - + +
366B ARG* 1.3 101.2 - - - +
368B SER* 1.3 61.6 + - - +
370B LEU* 3.2 9.7 + - + +
371B ARG* 3.0 25.8 + - - +
384B PHE* 4.0 41.0 - - + +
385B VAL* 6.3 1.1 - - + -
387B ALA* 5.0 3.5 - - + +
388B PRO* 3.8 30.5 - - + -
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Residues in contact with SER 368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B LEU* 3.2 46.3 - - - +
331B VAL* 4.4 2.5 - - - -
332B ARG* 3.5 16.0 - - - +
364B VAL 3.0 16.1 + - - -
365B LEU* 3.8 8.4 - - - -
367B LEU* 1.3 76.6 - - - +
369B ALA* 1.3 62.5 + - - +
371B ARG* 3.3 5.6 + - - +
372B GLY 2.9 18.7 + - - -
384B PHE* 3.6 12.7 - - - -
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Residues in contact with ALA 369 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331B VAL* 3.7 21.4 - - + +
335B GLY* 3.5 8.1 - - - -
349B LEU* 3.9 11.7 - - + +
351B VAL* 3.7 24.5 - - + -
365B LEU 3.0 17.6 + - - +
366B ARG 3.7 2.7 - - - +
367B LEU 3.4 0.2 - - - -
368B SER* 1.3 76.3 - - - +
370B LEU* 1.3 57.2 + - - +
372B GLY 3.2 1.3 + - - +
373B LEU* 2.8 27.5 + - - +
415B VAL* 4.3 9.4 - - + -
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Residues in contact with LEU 370 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349B LEU* 3.8 21.1 - - + -
366B ARG* 3.1 23.3 + - + +
367B LEU* 3.5 13.7 - - + +
369B ALA* 1.3 78.4 - - - +
371B ARG* 1.3 58.2 + - - +
373B LEU* 3.0 5.7 + - + +
374B PHE* 2.9 60.5 + - + -
387B ALA* 4.4 11.0 - - + +
388B PRO* 4.8 10.8 - - + -
391B ALA* 4.2 16.6 - - + -
396B VAL* 4.5 10.1 - - + -
398B ALA* 4.0 26.5 - - + -
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Residues in contact with ARG 371 (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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307B GLU* 4.7 20.6 + - - +
308B PHE* 5.6 4.9 - - - +
332B ARG* 4.2 26.1 - - + +
367B LEU 3.0 14.7 + - - +
368B SER* 3.6 5.4 - - - +
370B LEU* 1.3 82.4 - - - +
372B GLY* 1.3 59.1 + - - +
374B PHE 4.1 0.3 - - - -
375B SER* 3.2 25.0 + - - -
382B VAL* 3.2 43.2 + - + +
383B THR* 4.6 7.8 - - - +
384B PHE* 3.8 33.5 - - + -
387B ALA* 4.5 3.1 - - + +
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Residues in contact with GLY 372 (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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332B ARG* 3.4 29.6 - - - +
336B VAL* 3.4 25.7 - - - -
368B SER 2.9 12.7 + - - -
369B ALA 3.6 2.0 - - - -
371B ARG* 1.3 74.5 - - - +
373B LEU* 1.3 65.3 + - - +
375B SER* 3.3 15.3 + - - -
376B ALA 3.4 4.2 + - - -
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Residues in contact with LEU 373 (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 3.5 9.1 - - - +
338B ALA 4.9 0.4 - - - -
339B GLY* 3.5 29.2 - - - +
345B LEU* 4.9 4.7 - - + -
346B PRO* 3.7 32.1 - - + -
349B LEU* 4.2 24.9 - - + -
369B ALA 2.8 13.4 + - - +
370B LEU* 3.0 13.4 + - + +
372B GLY* 1.3 77.8 - - - +
374B PHE* 1.3 77.5 + - + +
376B ALA* 3.5 8.8 + - - +
377B VAL* 3.7 12.1 - - + +
396B VAL* 4.3 20.2 - - + -
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Residues in contact with PHE 374 (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 LEU* 4.9 7.0 - - + -
370B LEU* 2.9 40.6 + - + +
373B LEU* 1.3 84.2 - - + +
375B SER* 1.3 61.5 + - - +
376B ALA 3.2 1.6 - - - -
377B VAL* 3.8 6.7 - - + -
378B ILE* 2.9 49.3 + - + +
382B VAL* 4.1 10.9 - - + +
387B ALA* 4.2 7.2 - - + -
390B LEU* 3.9 22.9 - - + -
391B ALA* 3.4 44.4 - - + -
394B ARG* 4.2 20.2 - - + -
396B VAL* 4.0 20.9 - - + -
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Residues in contact with SER 375 (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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332B ARG* 5.6 2.4 + - - -
336B VAL* 4.0 11.8 - - - +
371B ARG* 3.2 18.6 + - - -
372B GLY* 3.3 8.8 + - - -
374B PHE* 1.3 72.8 - - - +
376B ALA* 1.3 61.6 + - - +
377B VAL 2.9 11.3 + - - -
378B ILE 3.6 12.5 + - - +
382B VAL* 4.3 13.4 - - - +
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Residues in contact with ALA 376 (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* 3.8 17.9 - - + +
339B GLY* 4.9 1.4 - - - -
340B VAL* 3.8 34.6 + - + +
372B GLY 3.4 13.6 + - - +
373B LEU 3.7 5.8 - - - +
374B PHE 3.2 0.6 - - - -
375B SER* 1.3 80.7 + - - +
377B VAL* 1.3 65.4 + - + +
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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