Contacts of the helix formed by residues 365 - 382 (chain B) in PDB entry 3DL2
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 365 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364B VAL* 1.3 76.6 - - - +
366B HIS* 1.3 63.8 + - - +
367B THR* 3.0 26.0 + - - +
368B SER* 3.2 18.5 + - - -
369B GLN* 3.1 21.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 366 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364B VAL 3.3 9.8 + - - -
365B SER* 1.3 71.0 + - - +
367B THR* 1.3 61.1 + - + +
369B GLN* 3.2 16.5 + - - +
370B VAL* 2.9 37.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 367 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365B SER* 3.0 12.3 + - - +
366B HIS* 1.3 78.7 - - + +
368B SER* 1.3 62.4 + - - +
370B VAL* 3.4 6.8 + - - +
371B GLN* 2.9 46.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 368 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364B VAL* 4.6 9.2 - - - -
365B SER* 3.2 23.2 + - - -
367B THR* 1.3 82.1 + - - +
369B GLN* 1.3 57.8 + - - +
371B GLN* 3.4 12.7 + - - +
372B LEU* 2.9 30.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 369 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B GLU* 5.5 2.2 + - - -
357B TRP* 3.6 56.7 - - + +
364B VAL* 3.9 29.1 - - + +
365B SER 3.1 17.2 + - - +
366B HIS* 3.2 15.2 + - - +
368B SER* 1.3 75.8 - - - +
370B VAL* 1.3 55.7 + - + +
372B LEU* 3.7 7.7 - - + +
373B SER* 2.8 37.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 370 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366B HIS* 2.9 25.7 + - + +
367B THR* 3.7 6.7 - - - +
369B GLN* 1.3 74.1 - - + +
371B GLN* 1.3 62.1 + - + +
373B SER* 3.3 5.5 + - - -
374B ASN* 2.8 50.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 371 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367B THR* 2.9 33.2 + - - +
368B SER* 3.7 12.5 + - - +
370B VAL* 1.3 77.9 - - + +
372B LEU* 1.3 61.8 + - - +
374B ASN* 3.5 7.7 + - - +
375B ARG* 3.1 63.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 372 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330B ILE* 4.3 26.2 - - + -
334B LEU* 3.8 25.8 - - + -
336B ALA* 4.0 22.9 - - + -
337B GLN 5.1 2.7 - - - +
338B THR* 4.6 6.3 - - - +
357B TRP* 4.3 18.4 - - + -
368B SER 2.9 20.8 + - - +
369B GLN* 3.7 7.4 - - + +
371B GLN* 1.3 72.5 - - - +
373B SER* 1.3 58.1 + - - +
375B ARG* 3.4 7.8 + - - +
376B ALA* 3.0 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 373 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330B ILE* 5.7 1.1 - - - -
355B LEU* 3.8 29.2 - - - +
357B TRP* 3.1 30.9 + - - -
369B GLN* 2.8 22.5 + - - +
370B VAL* 3.6 6.5 - - - -
372B LEU* 1.3 74.7 - - - +
374B ASN* 1.3 61.8 + - - +
376B ALA* 3.8 3.4 - - - +
377B MET* 2.9 32.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 374 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370B VAL* 2.8 43.7 + - - +
371B GLN* 3.8 8.1 - - - +
373B SER* 1.3 73.8 - - - +
375B ARG* 1.3 59.6 + - + +
377B MET* 3.4 6.7 + - - +
378B GLU* 3.0 37.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 375 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334B LEU* 4.9 9.9 - - + -
371B GLN* 3.1 54.1 + - - +
372B LEU* 3.7 7.6 - - - +
374B ASN* 1.3 79.1 - - + +
376B ALA* 1.3 64.2 + - - +
378B GLU* 3.3 9.0 + - - +
379B LEU* 3.1 30.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 376 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326B LEU* 3.6 19.7 - - + +
329B ILE* 4.0 18.8 - - + +
330B ILE* 3.7 26.5 - - + -
334B LEU* 4.2 6.6 - - + +
372B LEU 3.0 17.2 + - - +
373B SER* 4.0 2.5 - - - +
375B ARG* 1.3 75.8 - - - +
377B MET* 1.3 57.7 + - - +
379B LEU* 3.3 4.6 + - - +
380B LEU* 3.0 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 377 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326B LEU* 3.8 4.4 - - + +
345B VAL* 4.0 16.6 - - + -
353B LYS* 3.5 52.7 - - + +
355B LEU* 3.6 35.2 - - + -
373B SER 2.9 19.9 + - - +
374B ASN* 3.6 7.0 - - - +
375B ARG 3.2 0.2 - - - -
376B ALA* 1.3 77.6 - - - +
378B GLU* 1.3 56.8 + - + +
380B LEU* 3.3 7.3 + - + +
381B ARG* 2.9 47.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 378 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374B ASN* 3.0 23.9 + - + +
375B ARG* 3.3 7.4 + - - +
377B MET* 1.3 73.4 - - + +
379B LEU* 1.3 67.8 + - + +
381B ARG* 3.1 40.6 + - - +
382B VAL* 3.6 15.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 379 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329B ILE* 3.7 31.4 - - + -
333B VAL* 4.3 12.3 - - + -
334B LEU* 3.8 24.9 - - + -
375B ARG* 3.1 16.3 + - + +
376B ALA 3.6 6.5 - - - +
378B GLU* 1.3 77.2 - - + +
380B LEU* 1.3 61.9 + - - +
382B VAL* 3.5 20.3 - - + +
383B LYS* 3.6 16.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 380 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322B ASP* 3.7 31.4 - - + +
325B ARG* 3.5 44.1 + - + +
326B LEU* 4.2 9.4 - - + +
329B ILE* 3.8 12.3 - - + +
345B VAL* 3.9 16.6 - - + -
353B LYS* 3.8 25.8 - - + -
376B ALA 3.0 17.4 + - - +
377B MET* 3.6 10.8 - - - +
378B GLU 3.2 0.2 - - - -
379B LEU* 1.3 78.2 - - - +
381B ARG* 1.3 62.5 + - - +
383B LYS* 3.2 25.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 381 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351B GLU* 2.7 37.7 + - - +
352B ASP* 3.6 17.0 + - - +
353B LYS* 3.9 20.8 - - + +
377B MET* 2.9 50.3 + - - +
378B GLU* 3.1 33.1 + - - +
380B LEU* 1.3 75.3 - - - +
382B VAL* 1.3 60.2 + - - +
383B LYS 3.2 5.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 382 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378B GLU 3.6 10.3 + - - +
379B LEU* 3.5 22.0 - - + +
381B ARG* 1.3 77.2 - - - +
383B LYS* 1.3 66.7 + - + +
384B GLY 3.7 1.0 + - - -
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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