Contacts of the helix formed by residues 392 - 406 (chain B) in PDB entry 5T0I
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 GLY 392 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356B PRO* 4.3 10.9 - - - +
361B LYS* 4.8 9.3 - - - +
364B ILE* 4.5 25.6 - - - +
390B LEU 3.9 0.2 + - - -
391B SER* 1.3 70.5 - - - +
393B ALA* 1.3 65.4 + - - +
394B ASP 3.6 0.2 - - - -
395B ILE* 3.1 30.2 - - - +
396B LYS* 4.2 0.9 + - - +
310C ARG* 3.7 9.3 + - - -
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Residues in contact with ALA 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B PRO* 5.0 9.9 - - + -
391B SER* 3.0 19.7 + - - +
392B GLY* 1.3 80.9 - - - +
394B ASP* 1.3 69.9 + - - +
395B ILE 3.2 0.5 + - - -
396B LYS* 3.4 11.1 + - - +
397B ALA* 3.9 2.1 + - - +
308C PRO* 4.1 18.1 - - + +
310C ARG* 3.3 37.7 + - - +
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Residues in contact with ASP 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387B LYS* 5.8 0.7 - - - -
390B LEU* 3.2 34.5 - - + +
391B SER 3.7 2.6 + - - -
393B ALA* 1.3 80.1 - - - +
395B ILE* 1.3 58.1 + - - +
396B LYS 3.1 2.7 - - - -
397B ALA* 3.0 11.9 + - + +
398B ILE* 2.9 33.2 + - + +
426B VAL* 4.7 19.4 - - + +
429B LYS* 6.1 1.4 - - - +
430B LYS* 5.5 2.6 - - - +
308C PRO* 2.8 28.8 - - - +
309C GLY* 4.8 0.3 - - - -
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Residues in contact with ILE 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361B LYS* 5.1 5.2 - - + +
364B ILE* 5.1 4.5 - - + -
365B PHE* 3.8 42.7 - - + -
380B LEU* 6.0 0.4 - - + -
383B LEU* 4.6 13.2 - - + -
384B ILE* 4.8 13.5 - - + -
387B LYS* 3.7 34.5 - - - +
391B SER 4.4 2.7 + - - +
392B GLY* 3.1 32.8 + - - +
393B ALA 3.2 0.2 - - - -
394B ASP* 1.3 78.3 - - - +
396B LYS* 1.3 59.3 + - + +
398B ILE* 3.2 13.7 - - + +
399B CYS* 3.2 23.9 - - - -
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Residues in contact with LYS 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365B PHE* 4.9 7.3 - - + -
368B HIS* 3.6 49.8 + - - +
369B THR* 5.1 6.5 - - - +
392B GLY 4.9 1.3 - - - +
393B ALA 3.4 9.3 + - - +
394B ASP 3.1 0.4 - - - -
395B ILE* 1.3 83.1 - - + +
397B ALA* 1.3 51.7 + - - +
399B CYS* 3.3 6.1 + - + +
400B THR* 2.5 46.8 + - - +
180C ILE* 5.4 4.5 - - + -
181C ALA* 6.1 4.5 - - + -
310C ARG* 4.4 24.0 - - + +
311C ILE* 4.6 13.9 - - + -
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Residues in contact with ALA 397 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393B ALA 3.9 1.8 + - - +
394B ASP* 3.0 22.4 + - + +
396B LYS* 1.3 76.8 - - - +
398B ILE* 1.3 61.8 + - + +
400B THR* 3.1 10.6 + - - -
401B GLU* 3.0 30.1 + - - +
426B VAL* 6.0 2.7 - - + -
308C PRO 4.3 0.7 - - - +
309C GLY* 3.3 35.6 - - - +
310C ARG* 5.5 1.2 - - - +
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Residues in contact with ILE 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383B LEU* 5.6 4.0 - - + -
387B LYS* 3.5 39.0 - - + +
394B ASP 2.9 15.8 + - - +
395B ILE* 3.2 17.7 - - + +
397B ALA* 1.3 76.8 - - + +
399B CYS* 1.3 66.9 + - - +
401B GLU* 3.2 15.7 - - - +
402B ALA* 3.0 24.6 + - - +
419B PHE* 5.5 2.1 - - - -
423B LYS* 3.7 27.8 - - + -
426B VAL* 3.6 39.7 - - + -
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Residues in contact with CYS 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365B PHE* 3.4 32.1 - - + -
374B LEU* 3.6 25.9 - - + +
378B VAL* 6.3 0.4 - - - -
383B LEU* 5.2 9.0 - - - -
395B ILE* 3.2 23.5 + - - +
396B LYS* 3.3 6.0 + - + +
397B ALA 3.2 0.2 - - - -
398B ILE* 1.3 86.9 - - - +
400B THR* 1.3 66.2 + - - +
402B ALA* 3.3 18.9 + - - +
403B GLY* 3.6 4.0 + - - -
179C GLY 5.6 1.7 - - - +
180C ILE* 5.1 2.7 - - - +
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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
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396B LYS* 2.5 29.3 + - - +
397B ALA* 3.1 10.4 + - - -
399B CYS* 1.3 74.4 - - - +
401B GLU* 1.3 59.0 + - + +
403B GLY* 4.6 0.2 - - - -
404B LEU* 3.1 29.9 + - + +
180C ILE* 3.5 35.2 - - + +
309C GLY 5.1 1.1 - - - +
311C ILE* 3.3 38.7 - - + +
312C ASP 5.2 6.7 - - - +
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Residues in contact with GLU 401 (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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397B ALA 3.0 14.5 + - - +
398B ILE* 3.2 23.2 - - - +
400B THR* 1.3 76.1 - - + +
402B ALA* 1.3 59.3 + - - +
404B LEU* 3.6 19.3 - - + -
405B MET* 2.9 31.9 + - + +
422B SER* 4.0 22.8 - - - +
423B LYS* 5.1 1.7 - - - +
425B ASN* 5.4 4.5 + - - +
426B VAL* 3.3 29.0 - - - +
314C LYS* 5.8 3.6 - - - +
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Residues in contact with ALA 402 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374B LEU* 4.0 18.8 - - + -
398B ILE 3.0 19.0 + - - +
399B CYS* 3.5 13.5 - - - +
400B THR 3.2 0.8 - - - -
401B GLU* 1.3 78.9 - - - +
403B GLY* 1.3 61.6 + - - +
405B MET* 4.3 2.2 - - - +
406B ALA* 3.3 21.8 + - - +
419B PHE* 4.4 23.4 - - + -
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Residues in contact with GLY 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374B LEU* 4.7 13.8 - - - +
399B CYS 3.6 7.8 + - - -
400B THR 4.3 0.9 - - - -
402B ALA* 1.3 76.7 - - - +
404B LEU* 1.3 58.6 + - - +
406B ALA* 3.8 9.3 - - - +
407B LEU* 3.1 27.3 + - - +
411B ARG 5.0 3.5 - - - +
412B MET* 6.1 3.8 - - - -
178C LEU* 5.4 11.9 - - - +
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Residues in contact with LEU 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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400B THR* 3.1 25.1 + - + +
401B GLU* 3.6 20.0 - - + -
402B ALA 3.2 0.8 - - - -
403B GLY* 1.3 75.0 - - - +
405B MET* 1.3 63.9 + - - +
407B LEU* 3.2 32.6 + - + +
408B ARG* 4.0 6.9 + - - +
160C GLU 5.1 1.3 - - - +
163C GLU* 5.1 6.1 - - + -
164C VAL* 5.0 7.4 - - + -
312C ASP 5.6 1.6 - - - +
313C ARG* 3.3 61.6 + - - +
314C LYS* 5.1 0.7 - - + +
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Residues in contact with MET 405 (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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401B GLU* 2.9 18.7 + - + +
402B ALA* 4.3 2.2 - - - +
404B LEU* 1.3 77.4 - - - +
406B ALA* 1.3 60.8 + - - +
408B ARG* 3.3 42.0 + - + +
409B GLU* 4.4 2.8 - - - +
418B ASP* 3.3 39.3 - - - +
422B SER* 5.4 11.0 - - - +
313C ARG* 6.3 0.9 - - - +
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Residues in contact with ALA 406 (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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402B ALA 3.3 16.8 + - - +
403B GLY* 3.8 8.7 - - - +
404B LEU 3.3 0.2 - - - -
405B MET* 1.3 78.2 - - - +
407B LEU* 1.3 55.6 + - - +
408B ARG 3.1 1.6 - - - -
409B GLU* 3.0 34.6 + - - +
410B ARG 3.6 1.7 + - - -
411B ARG 3.9 18.2 - - - +
412B MET* 5.0 1.1 - - + -
413B LYS 3.3 26.7 - - - +
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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