Contacts of the helix formed by residues 353 - 364 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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230C GLU* 2.7 35.5 + - - +
351C PHE 3.4 8.3 + - - +
352C VAL* 1.3 77.9 - - - +
354C GLU* 1.3 66.2 + - - +
355C GLY 4.2 2.9 - - - -
356C ALA* 2.9 18.8 + - - +
357C ARG* 2.9 21.8 + - - +
382C TRP* 3.7 4.2 + - - -
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Residues in contact with GLU 354 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352C VAL 4.0 0.2 + - - -
353C THR* 1.3 72.7 - - - +
355C GLY* 1.3 60.3 + - - +
357C ARG* 3.5 16.3 + - + +
358C ASP* 3.2 22.3 + - - +
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Residues in contact with GLY 355 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353C THR* 3.1 3.4 + - - -
354C GLU* 1.3 76.9 - - - +
356C ALA* 1.3 64.4 + - - +
358C ASP* 3.2 15.4 + - - +
359C LEU* 3.3 11.6 + - - +
380C HIS* 3.7 8.1 + - - -
382C TRP* 4.0 22.6 - - - +
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Residues in contact with ALA 356 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230C GLU* 5.9 0.4 - - + -
319C CYS* 5.6 0.4 - - - -
323C LEU* 3.8 19.7 - - + -
352C VAL* 3.3 20.9 - - + -
353C THR* 2.9 23.4 + - - +
355C GLY* 1.3 75.0 - - - +
357C ARG* 1.3 62.7 + - - +
359C LEU* 3.2 3.6 + - - +
360C ILE* 3.1 29.1 + - - +
382C TRP* 3.7 21.4 - - + -
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Residues in contact with ARG 357 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348C PHE* 3.4 56.0 + - + +
349C PRO 3.3 22.8 + - - -
350C ASP* 4.2 12.3 + - - +
352C VAL* 3.2 20.7 + - + +
353C THR 2.9 15.6 + - - +
354C GLU* 3.6 17.2 - - + +
355C GLY 3.3 0.2 - - - -
356C ALA* 1.3 75.3 - - - +
358C ASP* 1.3 57.5 + - - +
360C ILE* 4.0 0.2 - - - +
361C SER* 2.8 39.1 + - - +
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Residues in contact with ASP 358 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354C GLU 3.2 11.1 + - - +
355C GLY* 3.2 11.6 + - - +
357C ARG* 1.3 78.9 - - - +
359C LEU* 1.3 62.1 + - - +
361C SER* 4.1 3.2 - - - -
362C ARG* 3.1 49.3 + - - +
380C HIS* 3.5 15.6 - - - +
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Residues in contact with LEU 359 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237C ILE* 4.8 3.6 - - + -
319C CYS* 4.6 9.2 - - - -
355C GLY 3.3 5.0 + - - +
356C ALA 3.2 8.8 + - - +
358C ASP* 1.3 78.4 - - - +
360C ILE* 1.3 63.6 + - + +
362C ARG* 3.6 4.3 + - + +
363C LEU* 3.1 46.5 + - + +
372C PRO* 5.6 2.9 - - + -
377C VAL* 4.0 26.2 - - + -
380C HIS* 3.7 33.6 + - + +
382C TRP* 3.5 31.6 - - + -
383C ILE* 3.6 20.9 - - + -
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Residues in contact with ILE 360 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316C GLY* 4.1 6.5 - - - +
319C CYS* 4.0 29.4 - - + -
320C TYR* 3.9 27.4 - - + +
323C LEU* 4.3 13.2 - - + -
346C PHE* 4.1 1.1 - - + -
348C PHE* 3.7 36.3 - - + -
352C VAL* 4.9 1.3 - - + -
356C ALA 3.1 17.0 + - - +
359C LEU* 1.3 72.7 - - - +
361C SER* 1.3 56.6 + - - +
363C LEU* 3.1 7.2 + - - -
364C LEU* 2.7 59.6 + - + +
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Residues in contact with SER 361 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346C PHE* 4.4 13.9 - - - -
348C PHE* 3.6 18.5 - - - -
357C ARG* 2.8 28.9 + - - +
358C ASP* 4.1 4.3 - - - -
360C ILE* 1.3 73.3 - - - +
362C ARG* 1.3 63.5 + - - +
364C LEU 3.7 6.4 + - - +
365C LYS* 3.6 22.2 + - - +
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Residues in contact with ARG 362 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358C ASP* 3.1 35.8 + - - +
359C LEU* 3.8 5.2 - - + +
361C SER* 1.3 77.5 - - - +
363C LEU* 1.3 61.9 + - - +
365C LYS* 3.1 27.3 - - - +
370C GLN 4.1 3.2 - - - +
371C ARG* 3.8 2.8 - - - -
372C PRO* 3.5 33.4 - - + +
376C GLU* 5.8 2.8 + - - +
380C HIS* 3.7 27.6 + - - -
381C PRO* 6.0 0.6 - - - +
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Residues in contact with LEU 363 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237C ILE* 5.9 1.3 - - + -
312C LEU* 3.2 42.2 - - + +
313C TRP* 4.1 6.4 - - - -
315C LEU* 4.3 10.5 - - + +
316C GLY* 3.7 25.4 - - - +
319C CYS* 5.4 2.9 - - + -
359C LEU* 3.1 41.4 + - + +
360C ILE* 3.1 5.3 + - - +
362C ARG* 1.3 75.9 - - - +
364C LEU* 1.3 59.1 + - - +
365C LYS 2.9 10.9 + - - -
371C ARG* 3.3 23.4 + - - +
372C PRO* 3.7 26.5 - - + -
377C VAL* 3.9 9.4 - - + -
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Residues in contact with LEU 364 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313C TRP* 3.6 29.4 - - + +
316C GLY* 3.5 6.1 - - - +
317C VAL* 3.3 36.1 - - + +
328C PRO* 4.0 22.9 - - + -
329C PHE* 4.2 4.5 - - + -
344C VAL* 3.1 24.6 - - - +
346C PHE* 3.7 28.7 - - + -
360C ILE* 2.7 43.7 + - + +
361C SER 3.8 5.9 - - - +
363C LEU* 1.3 70.2 - - - +
365C 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