Contacts of the helix formed by residues 395 - 413 (chain B) in PDB entry 5DO7
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 ALA 395 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394B GLY* 1.3 68.5 - - - -
396B VAL* 1.3 56.6 + - + +
398B GLN* 2.8 15.2 + - - +
399B PHE* 2.6 38.2 + - - +
487B TYR* 4.1 20.0 - - + -
489B THR* 5.8 2.7 - - + -
490B GLY* 4.8 23.5 - - - +
491B PRO* 5.2 1.5 - - - +
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Residues in contact with VAL 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394B GLY 3.4 0.9 - - - -
395B ALA* 1.3 77.3 - - + +
397B GLN* 1.3 65.7 + - - +
399B PHE* 3.1 8.4 + - + +
400B THR* 3.0 36.5 + - + +
490B GLY 5.7 0.2 - - - -
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Residues in contact with GLN 397 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B GLN* 4.2 31.3 + - - +
175B LEU 5.4 1.2 - - - +
176B PRO 5.4 0.3 - - - -
177B ARG* 3.9 31.0 + - + +
184B ARG* 3.8 24.2 - - - +
394B GLY* 2.8 19.7 + - - +
396B VAL* 1.3 77.6 - - - +
398B GLN* 1.3 66.9 + - + +
400B THR* 3.0 22.3 + - - +
401B THR* 3.1 12.8 + - - +
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Residues in contact with GLN 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B GLN 6.1 0.2 - - - -
173B MET* 4.3 29.6 + - + +
394B GLY 2.7 24.8 + - - +
395B ALA* 3.2 5.8 - - - +
397B GLN* 1.3 71.8 - - + +
399B PHE* 1.3 66.8 + - - +
401B THR* 2.8 17.2 + - - -
402B LEU* 3.0 20.1 + - + +
484B ASP 5.0 3.0 + - - -
485B GLY 3.6 24.2 + - - +
486B LEU* 4.1 1.7 - - - +
487B TYR* 2.9 55.2 + - - +
491B PRO* 4.4 5.3 - - + +
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Residues in contact with PHE 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395B ALA 2.6 15.8 + - - +
396B VAL* 3.4 13.5 - - + +
398B GLN* 1.3 74.1 - - - +
400B THR* 1.3 71.9 + - + +
402B LEU* 3.2 4.4 + - - +
403B ILE* 3.1 34.7 + - + +
490B GLY 3.9 14.8 - - - +
491B PRO* 3.4 24.0 - - - +
494B PHE* 3.2 41.5 - + + -
495B ALA* 3.4 5.4 - - - -
498B LEU* 3.7 28.5 - - + -
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Residues in contact with THR 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396B VAL* 3.0 25.5 + - + +
397B GLN* 3.0 14.6 + - - +
399B PHE* 1.3 81.5 - - + +
401B THR* 1.3 77.4 + - - +
403B ILE* 2.8 15.5 + - - +
404B ARG* 2.8 44.0 + - - +
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Residues in contact with THR 401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B PHE* 3.3 40.7 - - + +
172B GLN* 4.1 22.4 + - + +
173B MET* 3.8 24.3 - - + +
397B GLN* 3.1 13.4 + - - +
398B GLN 2.8 13.4 + - - -
400B THR* 1.3 77.2 + - - +
402B LEU* 1.3 66.2 + - - +
404B ARG* 2.8 10.6 + - - +
405B ARG* 2.8 24.1 + - + +
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Residues in contact with LEU 402 (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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173B MET* 3.9 20.2 - - + -
398B GLN* 3.0 16.0 + - + +
399B PHE* 3.4 7.6 - - - +
401B THR* 1.3 80.2 - - - +
403B ILE* 1.3 58.7 + - - +
405B ARG* 3.6 25.6 + - - +
406B GLN* 2.8 35.0 + - + +
486B LEU* 3.1 41.3 - - + -
491B PRO* 3.4 28.0 - - + +
492B TYR* 4.0 3.8 - - + -
495B ALA* 3.8 18.2 - - + -
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Residues in contact with ILE 403 (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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399B PHE* 3.1 39.1 + - + +
400B THR* 2.8 25.6 + - - +
402B LEU* 1.3 75.5 - - - +
404B ARG* 1.3 85.4 + - - +
406B GLN* 4.3 6.3 - - - -
407B ILE* 2.8 51.7 + - + +
494B PHE 4.4 0.9 - - - +
495B ALA* 3.4 24.5 - - - +
498B LEU* 4.6 8.7 - - + -
499B GLY* 4.7 1.8 - - - +
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Residues in contact with ARG 404 (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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169B PHE* 3.9 22.0 - - + -
400B THR* 2.8 41.3 + - - +
401B THR* 2.8 9.7 + - - +
403B ILE* 1.3 99.7 - - - +
405B ARG* 1.3 56.9 + - - +
407B ILE* 3.4 6.2 - - + +
408B SER* 2.8 38.7 + - - +
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Residues in contact with ARG 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B LEU* 3.7 22.4 - - + +
161B LEU* 3.8 14.8 - - + +
166B THR* 5.6 6.9 - - - +
169B PHE* 3.7 49.6 + - + +
170B ILE* 5.5 5.4 - - - +
173B MET* 4.2 15.6 - - - +
401B THR* 2.8 19.4 + - + +
402B LEU* 3.6 28.7 + - - +
404B ARG* 1.3 72.3 - - - +
406B GLN* 1.3 67.8 + - - +
407B ILE 3.2 0.7 + - - -
408B SER* 3.2 10.3 + - - -
409B ASN* 3.2 15.8 + - - +
480B TYR* 2.7 50.6 + - - -
486B LEU* 5.0 0.8 - - - +
492B TYR* 5.6 3.4 - - - -
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Residues in contact with GLN 406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B LEU* 5.1 8.1 - - - -
402B LEU* 2.8 24.9 + - + +
403B ILE* 3.9 3.1 - - - +
405B ARG* 1.3 78.4 - - - +
407B ILE* 1.3 61.3 + - - +
409B ASN* 4.2 2.8 - - - +
410B ASP* 3.3 38.5 + - - +
474B GLU* 4.7 10.6 - - - +
495B ALA* 4.5 10.3 - - + +
496B LYS* 4.9 16.6 - - - +
499B GLY* 4.1 34.4 + - - -
500B GLU* 4.6 3.8 + - - +
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Residues in contact with ILE 407 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403B ILE* 2.8 37.8 + - + +
404B ARG* 3.4 12.3 - - + +
406B GLN* 1.3 76.6 - - + +
408B SER* 1.3 66.7 + - - +
410B ASP* 4.1 1.7 - - + +
411B PHE* 2.8 46.6 + - + +
498B LEU 4.8 1.6 - - - +
499B GLY* 3.7 30.7 - - - +
502B PRO* 4.1 20.9 - - + -
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Residues in contact with SER 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B LEU* 4.1 17.5 - - - -
169B PHE* 4.4 9.5 - - - -
404B ARG* 2.8 26.1 + - - +
405B ARG* 3.5 5.8 - - - -
407B ILE* 1.3 78.1 - - - +
409B ASN* 1.3 64.8 + - - +
411B PHE* 2.8 9.0 + - - +
412B ARG* 2.8 35.2 + - - +
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Residues in contact with ASN 409 (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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158B LEU* 4.1 29.5 - - + +
159B PRO* 4.0 12.0 - - - +
160B ASN* 3.2 42.7 - - - +
161B LEU* 4.4 9.8 - - + +
405B ARG 3.2 11.6 + - - +
406B GLN 4.2 2.9 - - - +
408B SER* 1.3 77.5 - - - +
410B ASP* 1.3 58.6 + - - +
412B ARG* 2.8 12.4 + - - +
413B ASP* 2.8 33.2 + - - +
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Residues in contact with ASP 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406B GLN* 3.3 33.6 + - - +
407B ILE* 4.1 3.4 - - + +
408B SER 3.3 0.8 - - - -
409B ASN* 1.3 85.4 - - - +
411B PHE* 1.3 67.6 + - + +
413B ASP* 3.4 21.7 - - - +
416B THR* 4.3 14.6 - - - +
417B LEU* 4.2 9.7 - - - +
470B LYS* 4.0 13.5 + - - +
499B GLY 4.8 5.6 - - - +
500B GLU* 5.0 3.8 - - - +
503B GLU* 3.4 26.1 - - - +
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Residues in contact with PHE 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407B ILE* 2.8 29.1 + - + +
408B SER* 2.8 7.7 + - - +
410B ASP* 1.3 81.9 - - + +
412B ARG* 1.3 59.1 + - + +
413B ASP 3.2 10.7 + - - +
414B LEU* 4.7 4.2 + - - +
417B LEU* 4.0 26.1 - - + +
499B GLY 5.8 1.1 - - - -
502B PRO* 4.1 31.4 - - + -
503B GLU* 4.2 19.7 - - + -
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Residues in contact with ARG 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B ASN* 3.0 30.6 + - + -
161B LEU* 3.9 4.0 - - - +
162B THR* 4.5 6.5 - - - +
165B GLU* 3.1 34.7 + - - -
204B ARG* 3.3 41.2 + - - +
408B SER* 2.8 42.4 + - - +
409B ASN 2.8 6.0 + - - +
411B PHE* 1.3 69.9 - - + +
413B ASP* 1.3 60.2 + - - +
414B LEU* 3.3 8.3 + - - +
415B PRO* 5.3 0.2 - - - +
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Residues in contact with ASP 413 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B ASN* 3.4 19.9 + - - +
409B ASN* 2.8 8.8 + - - +
410B ASP* 3.4 22.2 - - - +
411B PHE 4.1 0.9 - - - -
412B ARG* 1.3 74.6 - - - +
414B LEU* 1.3 58.3 + - - +
415B PRO* 3.2 23.7 - - - +
416B THR* 2.8 34.6 + - + +
417B LEU* 3.3 22.5 + - - +
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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
------------------------------------------------------------
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