Contacts of the helix formed by residues 353 - 364 (chain B) in PDB entry 3H0Z
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 THR 353 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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230B GLU* 3.0 37.3 + - - +
351B PHE 3.8 11.9 - - - +
352B VAL* 1.3 76.9 - - - +
354B GLU* 1.3 59.3 + - - +
355B GLY 3.7 3.3 + - - -
356B ALA* 3.5 14.7 + - - +
357B ARG* 2.9 34.0 + - - +
382B TRP* 4.0 2.8 + - - -
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Residues in contact with GLU 354 (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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353B THR* 1.3 72.6 - - - +
355B GLY* 1.3 64.7 + - - +
357B ARG* 3.6 15.6 - - + +
358B ASP* 3.2 21.8 + - - +
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Residues in contact with GLY 355 (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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353B THR* 3.3 3.6 + - - -
354B GLU* 1.3 79.6 - - - +
356B ALA* 1.3 59.9 + - - +
358B ASP* 3.5 4.5 + - - +
359B LEU 3.4 5.9 + - - -
380B HIS* 3.2 25.1 + - - -
382B TRP* 3.4 23.1 - - - +
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Residues in contact with ALA 356 (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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230B GLU* 5.0 0.7 - - - +
319B CYS* 6.0 0.2 - - - -
323B LEU* 3.6 31.0 - - + -
352B VAL* 4.1 8.3 - - + -
353B THR* 3.5 11.5 + - - +
354B GLU 3.4 0.2 - - - -
355B GLY* 1.3 71.1 - - - +
357B ARG* 1.3 66.9 + - - +
358B ASP 3.1 2.2 + - - -
359B LEU* 3.2 1.2 + - - +
360B ILE* 2.9 33.4 + - + +
382B TRP* 3.6 29.7 - - + +
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Residues in contact with ARG 357 (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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348B PHE* 3.5 56.1 + - + +
349B PRO 3.1 28.7 + - - -
350B ASP* 3.8 9.9 + - - +
352B VAL* 3.3 20.0 + - + +
353B THR 2.9 22.1 + - - +
354B GLU* 3.6 15.0 - - + +
355B GLY 3.4 0.2 - - - -
356B ALA* 1.3 77.6 - - - +
358B ASP* 1.3 58.6 - - - +
361B SER* 2.8 30.7 + - - -
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Residues in contact with ASP 358 (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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354B GLU 3.2 13.4 + - - +
355B GLY* 3.6 10.5 - - - +
356B ALA 3.1 0.6 - - - -
357B ARG* 1.3 74.5 - - - +
359B LEU* 1.3 66.3 + - - +
361B SER* 3.1 5.2 + - - -
362B ARG* 3.0 47.0 + - - +
380B HIS* 3.1 23.1 - - + -
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Residues in contact with LEU 359 (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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237B ILE* 4.6 4.9 - - + -
319B CYS* 5.0 4.7 - - - -
355B GLY 3.4 4.2 + - - +
356B ALA 3.2 6.7 + - - +
358B ASP* 1.3 81.8 + - - +
360B ILE* 1.3 65.3 + - + +
362B ARG* 3.2 7.2 + - + +
363B LEU* 3.0 51.5 + - + +
372B PRO* 5.3 2.2 - - + -
377B VAL* 4.2 23.3 - - + -
380B HIS* 3.7 27.8 + - + +
382B TRP* 3.7 20.0 - - + -
383B ILE* 3.5 35.7 - - + -
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Residues in contact with ILE 360 (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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316B GLY* 4.3 7.0 - - - +
319B CYS* 3.8 30.3 - - + -
320B TYR* 3.8 28.5 - - + +
323B LEU* 4.4 11.4 - - + -
324B VAL* 6.0 0.9 - - + -
346B PHE* 4.1 2.9 - - + -
348B PHE* 3.7 34.1 - - + -
352B VAL* 5.0 2.0 - - + -
356B ALA* 2.9 19.9 + - + +
359B LEU* 1.3 75.6 - - + +
361B SER* 1.3 57.5 + - - +
363B LEU* 3.4 8.3 + - - +
364B LEU* 2.9 52.1 + - + +
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Residues in contact with SER 361 (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 PHE* 4.3 11.6 - - - -
348B PHE* 4.0 14.7 - - - -
357B ARG 2.8 21.0 + - - -
358B ASP* 3.1 6.5 + - - -
360B ILE* 1.3 77.0 - - - +
362B ARG* 1.3 66.0 + - - +
364B LEU 3.2 18.4 + - - +
365B LYS* 3.5 10.2 + - - +
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Residues in contact with ARG 362 (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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358B ASP* 3.0 37.0 + - - +
359B LEU* 3.6 9.9 - - + +
361B SER* 1.3 75.4 - - - +
363B LEU* 1.3 60.0 + - - +
365B LYS* 3.2 31.7 - - - +
370B GLN 4.0 1.7 - - - +
371B ARG* 3.6 4.3 - - - -
372B PRO* 3.4 35.8 - - + +
376B GLU* 4.6 16.6 + - - +
380B HIS* 5.0 10.6 + - - -
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Residues in contact with LEU 363 (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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237B ILE* 5.9 1.1 - - + -
312B LEU* 3.3 33.0 - - + +
313B TRP* 3.6 12.1 - - - -
315B LEU* 4.2 11.9 - - + +
316B GLY* 3.6 31.0 - - - +
319B CYS* 5.2 3.4 - - + -
359B LEU* 3.0 48.0 + - + +
360B ILE* 3.7 3.8 - - - +
362B ARG* 1.3 77.5 - - - +
364B LEU* 1.3 57.7 + - - +
365B LYS 3.3 3.8 + - - -
371B ARG* 3.5 20.5 + - - +
372B PRO* 4.1 9.6 - - + -
377B VAL* 3.9 24.9 - - + -
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Residues in contact with LEU 364 (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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313B TRP* 3.6 52.9 - - + +
316B GLY 4.2 5.8 - - - -
317B VAL* 3.8 14.4 - - + +
328B PRO* 4.2 14.6 - - + -
329B PHE* 3.9 13.7 - - + -
344B VAL* 3.3 24.0 - - + +
346B PHE* 3.8 27.1 - - + -
360B ILE* 2.9 38.1 + - + +
361B SER 3.2 7.2 + - - +
363B LEU* 1.3 74.9 - - - +
365B LYS* 1.3 58.0 + - - +
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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