Contacts of the helix formed by residues 372 - 388 (chain B) in PDB entry 4DQ6
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 372 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5B PHE 3.5 20.6 - - - +
6B ASN 3.7 15.0 - - - +
7B GLU 3.4 22.2 - - - +
8B ILE* 4.0 18.2 - - + -
9B VAL 5.2 1.3 - - - +
40B ASP* 3.5 22.9 - - + +
41B PHE* 3.5 1.3 - - + -
295B TYR* 3.7 2.0 - - - +
299B ASN* 4.5 0.2 - - - -
371B CYS* 1.4 91.3 - - + +
373B ARG* 1.3 66.7 + - - +
374B SER 4.2 2.7 - - - +
375B MET* 3.0 21.5 + - + +
376B LEU* 3.0 10.6 + - - +
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Residues in contact with ARG 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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6B ASN* 4.1 8.0 + - - +
295B TYR* 2.9 26.2 + - + +
298B SER* 2.9 45.5 + - - -
299B ASN* 2.9 24.3 + - - +
302B PHE* 3.7 51.3 - - - +
371B CYS 3.4 1.6 + - - -
372B PRO* 1.3 70.7 - - - +
374B SER* 1.4 59.5 + - - +
376B LEU* 3.1 3.9 + - - +
377B GLU* 2.8 31.3 + - + +
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Residues in contact with SER 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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6B ASN* 5.0 5.8 + - - +
8B ILE* 4.4 18.8 - - - +
372B PRO* 3.1 3.4 + - - +
373B ARG* 1.4 79.4 - - - +
375B MET* 1.3 56.6 + - - +
377B GLU* 3.5 9.7 + - - +
378B GLU* 3.1 33.7 + - - +
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Residues in contact with MET 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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8B ILE* 5.0 6.1 - - + +
18B LYS* 5.1 0.2 - - - -
19B TRP* 3.9 22.0 - - + -
32B LEU* 3.7 22.7 - - + +
33B PRO* 3.2 27.6 - - + +
34B MET* 3.7 7.2 - - - -
40B ASP* 3.2 31.2 - - - +
371B CYS* 3.8 14.1 - - + -
372B PRO* 3.0 21.2 + - + +
374B SER* 1.3 76.4 - - - +
376B LEU* 1.3 60.7 + - - +
378B GLU* 3.2 7.9 + - - +
379B ALA* 2.9 28.9 + - - +
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Residues in contact with LEU 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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34B MET* 3.9 15.9 - - + -
299B ASN* 3.5 50.7 - - + +
302B PHE* 4.0 11.7 - - + -
303B ALA* 4.3 3.1 - - + -
367B ILE* 5.2 1.3 - - + -
369B LEU* 3.8 27.4 - - + -
371B CYS* 3.8 12.0 - - - -
372B PRO 3.0 12.0 + - - +
373B ARG* 3.5 8.3 - - - +
375B MET* 1.3 77.1 - - - +
377B GLU* 1.3 61.4 + - - +
379B ALA* 3.2 4.8 + - + +
380B LEU* 3.0 42.8 + - + +
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Residues in contact with GLU 377 (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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302B PHE* 4.2 30.9 - - + -
306B TYR* 5.3 6.3 - - + -
373B ARG* 2.8 23.0 + - + +
374B SER* 3.7 8.9 - - - +
376B LEU* 1.3 73.1 - - - +
378B GLU* 1.3 63.6 + - - +
380B LEU* 3.3 4.6 + - - +
381B ILE* 3.0 41.8 + - + +
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Residues in contact with GLU 378 (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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32B LEU* 3.8 17.1 - - + +
374B SER* 3.1 17.6 + - - +
375B MET* 3.2 10.3 + - - +
377B GLU* 1.3 80.7 - - + +
379B ALA* 1.3 63.2 + - - +
381B ILE* 3.4 13.3 + - + +
382B ARG* 3.0 40.6 + - - +
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Residues in contact with ALA 379 (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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32B LEU* 3.6 11.3 - - + +
34B MET* 3.6 42.2 - - + -
349B VAL* 4.5 5.7 - - + +
367B ILE* 5.5 0.9 - - + -
375B MET 2.9 10.4 + - - +
376B LEU* 3.5 9.4 - - + +
378B GLU* 1.3 79.7 - - - +
380B LEU* 1.3 58.0 + - + +
382B ARG* 3.2 5.5 + - - +
383B ILE* 3.0 37.1 + - + +
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Residues in contact with LEU 380 (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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302B PHE* 3.7 30.3 - - + -
303B ALA* 3.9 22.2 - - + -
306B TYR* 3.7 26.0 - - + -
307B ILE* 4.1 29.4 - - + -
311B MET* 3.6 12.7 - - + +
325B LEU* 5.9 0.7 - - + -
367B ILE* 5.1 6.3 - - + -
376B LEU* 3.0 30.5 + - + +
377B GLU* 3.3 3.6 + - - +
379B ALA* 1.3 75.9 - - + +
381B ILE* 1.3 57.7 + - - +
383B ILE* 3.3 14.8 + - + -
384B LYS* 2.9 28.8 + - - +
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Residues in contact with ILE 381 (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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306B TYR* 3.6 22.0 - - + +
377B GLU* 3.0 44.2 + - + +
378B GLU* 3.6 12.3 - - + +
379B ALA 3.3 0.2 - - - -
380B LEU* 1.3 77.2 - - - +
382B ARG* 1.3 61.3 + - + +
384B LYS* 3.4 10.3 + - - +
385B ASN* 2.9 27.6 + - + +
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Residues in contact with ARG 382 (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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30B ASP 5.1 0.8 + - - -
31B LEU* 4.5 2.4 - - - +
32B LEU* 3.8 37.1 - - - +
347B GLY* 3.3 31.2 - - - +
348B LYS* 2.9 44.9 + - - +
349B VAL* 4.2 9.4 - - + -
378B GLU* 3.0 29.4 + - - +
379B ALA 3.6 4.9 - - - +
381B ILE* 1.3 77.4 - - + +
383B ILE* 1.3 62.0 + - - +
385B ASN* 3.2 6.7 + - - +
386B ALA 2.9 24.1 + - - -
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Residues in contact with ILE 383 (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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311B MET* 3.7 18.4 - - + -
314B LEU* 4.4 2.0 - - + -
329B PHE* 3.9 30.1 - - + -
343B LEU* 4.5 4.5 - - + -
349B VAL* 4.1 16.8 - - + -
351B LEU* 4.0 20.0 - - + -
367B ILE* 3.8 31.4 - - + -
379B ALA* 3.0 25.2 + - + +
380B LEU* 3.7 16.4 - - + +
382B ARG* 1.3 75.4 - - - +
384B LYS* 1.3 64.8 + - - +
386B ALA* 3.1 16.8 + - - +
387B ILE* 3.1 14.9 + - + +
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Residues in contact with LYS 384 (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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306B TYR* 3.2 24.3 + - + +
310B ASN* 3.8 41.9 + - + +
311B MET* 3.5 19.1 - - + -
380B LEU 2.9 17.2 + - - +
381B ILE* 3.5 10.3 - - - +
383B ILE* 1.3 76.7 - - - +
385B ASN* 1.3 60.0 + - - +
387B ILE* 3.4 1.0 + - - +
388B ASN* 2.9 44.7 + - + +
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Residues in contact with ASN 385 (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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346B LYS* 2.9 68.8 + - - +
347B GLY* 4.5 0.8 - - - -
348B LYS* 5.1 3.0 - - - +
381B ILE* 2.9 15.9 + - + +
382B ARG* 3.2 10.7 + - - +
384B LYS* 1.3 75.2 - - - +
386B ALA* 1.3 62.1 + - - +
387B ILE 3.3 0.7 + - - -
388B ASN* 3.4 13.1 + - - +
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Residues in contact with ALA 386 (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 ILE* 3.4 37.4 - - + +
343B LEU* 4.0 22.4 - - + -
346B LYS* 3.7 16.0 - - - +
347B GLY* 3.7 14.8 - - - +
382B ARG 2.9 14.2 + - - +
383B ILE 3.1 8.5 + - - +
385B ASN* 1.3 76.3 - - - +
387B ILE* 1.3 63.0 + - + +
388B ASN 3.6 1.7 + - - +
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Residues in contact with ILE 387 (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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311B MET* 3.8 31.6 - - + -
314B LEU* 4.1 22.9 - - + -
329B PHE* 4.2 15.5 - - + -
332B LEU* 3.7 35.4 - - + +
339B LEU* 4.9 0.9 - - + -
342B ILE* 4.2 14.1 - - + -
343B LEU* 5.1 0.9 - - + -
383B ILE* 3.1 14.6 + - + +
384B LYS* 3.7 6.3 - - - +
385B ASN 3.2 0.2 - - - -
386B ALA* 1.3 81.8 - - + +
388B ASN* 1.3 68.7 + - - +
402B CL 4.2 10.5 - - + -
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Residues in contact with ASN 388 (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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310B ASN 5.0 5.9 + - - -
311B MET* 5.2 0.4 - - - +
346B LYS* 3.7 24.1 + - - +
384B LYS* 2.9 40.6 + - + +
385B ASN* 3.6 13.7 - - - +
386B ALA 4.2 1.4 - - - +
387B ILE* 1.3 92.0 - - - +
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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