Contacts of the helix formed by residues 323 - 333 (chain C) in PDB entry 4HHM
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 ASP 323 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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319C ALA 3.0 18.4 + - - +
320C PHE 3.4 0.2 + - - -
322C ALA* 1.3 75.5 - - - +
324C PRO* 1.3 71.6 - - - +
325C GLU* 2.9 19.0 + - - +
326C VAL* 2.9 37.6 + - + +
327C GLN* 3.1 11.4 + - - +
378C LEU* 5.4 0.3 - - - +
382C HIS* 3.1 14.0 + - + +
387C ARG* 2.7 36.5 + - - -
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Residues in contact with PRO 324 (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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322C ALA 3.0 6.5 - - - +
323C ASP* 1.3 90.5 - - - +
325C GLU* 1.3 59.5 + - - +
327C GLN* 3.3 16.1 + - - +
328C GLU* 3.0 23.6 + - - +
331C ARG* 4.8 1.9 + - - -
322H ALA* 4.2 16.2 - - + +
324H PRO* 3.5 29.6 - - + -
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Residues in contact with GLU 325 (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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323C ASP* 2.9 16.8 + - - +
324C PRO* 1.3 80.4 - - - +
326C VAL* 1.3 55.8 + - - +
328C GLU* 3.4 8.2 + - + +
329C ALA* 3.0 26.3 + - - +
374C ARG* 3.4 29.4 + - - +
378C LEU* 4.5 10.7 - - + +
387C ARG* 3.4 24.6 + - - +
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Residues in contact with VAL 326 (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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320C PHE* 3.1 75.2 - - + +
321C ARG* 5.0 2.2 - - - -
323C ASP* 2.9 24.3 + - + +
325C GLU* 1.3 74.3 - - - +
327C GLN* 1.3 54.1 + - + +
329C ALA* 2.9 3.3 + - - +
330C LEU* 2.7 50.2 + - + +
375C LEU* 4.4 3.6 - - + -
378C LEU* 4.1 17.3 - - + -
382C HIS* 4.1 4.3 - - + +
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Residues in contact with GLN 327 (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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321C ARG 3.2 21.2 - - - +
322C ALA 3.3 4.1 - - - +
323C ASP 3.1 11.8 + - - +
324C PRO* 3.3 20.0 + - - +
326C VAL* 1.3 77.8 - - + +
328C GLU* 1.3 60.4 + - - +
330C LEU* 3.1 17.9 + - + +
331C ARG* 3.1 41.2 + - - +
321H ARG 5.0 0.2 + - - -
322H ALA* 4.0 11.5 + - - +
327H GLN* 2.5 48.0 + - - -
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Residues in contact with GLU 328 (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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324C PRO 3.0 13.2 + - - +
325C GLU* 3.6 11.7 - - + +
326C VAL 3.2 0.2 - - - -
327C GLN* 1.3 76.0 - - - +
329C ALA* 1.3 59.6 + - - +
331C ARG* 2.8 44.0 + - - +
332C ALA* 2.8 33.4 + - + +
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Residues in contact with ALA 329 (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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325C GLU 3.0 13.5 + - - +
326C VAL 2.9 9.5 + - - +
328C GLU* 1.3 74.4 - - - +
330C LEU* 1.3 65.4 + - - +
332C ALA* 3.3 9.9 + - - +
333C ALA* 3.1 22.7 + - - +
371C ALA* 5.1 2.2 - - - +
374C ARG* 5.0 10.8 - - - +
375C LEU* 3.9 20.8 - - + +
378C LEU* 3.6 23.8 - - + -
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Residues in contact with LEU 330 (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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321C ARG* 4.1 26.0 - - - +
326C VAL* 2.7 27.3 + - + +
327C GLN* 3.3 20.9 - - + +
329C ALA* 1.3 78.9 - - - +
331C ARG* 1.3 57.2 + - + +
333C ALA* 3.0 17.5 + - - +
334C ARG 3.0 9.2 + - - -
335C LEU* 3.2 35.3 + - + +
336C ASP 5.4 0.4 - - - -
375C LEU* 3.6 30.3 - - + -
147D ALA* 4.2 11.4 - - + +
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Residues in contact with ARG 331 (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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324C PRO 4.8 2.2 + - - -
327C GLN* 3.1 29.6 + - - +
328C GLU* 2.8 50.8 + - - +
330C LEU* 1.3 76.2 - - + +
332C ALA* 1.3 59.1 + - - +
334C ARG* 2.9 25.1 + - - +
336C ASP* 4.0 28.5 - - + +
321H ARG 6.0 0.6 + - - -
322H ALA* 4.9 18.5 - - - +
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Residues in contact with ALA 332 (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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328C GLU* 2.8 22.7 + - + +
329C ALA* 3.6 11.0 - - - +
330C LEU 3.2 0.2 - - - -
331C ARG* 1.3 76.9 - - - +
333C ALA* 1.3 57.8 + - - +
334C ARG* 3.1 23.1 + - - +
370C MET 4.1 2.5 - - - +
371C ALA* 4.4 15.4 - - + +
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Residues in contact with ALA 333 (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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329C ALA 3.1 10.8 + - - +
330C LEU 3.0 9.2 + - - +
332C ALA* 1.3 75.2 - - - +
334C ARG* 1.3 67.4 + - - +
335C LEU* 3.3 15.5 - - + -
370C MET* 3.2 30.2 - - - +
371C ALA 4.7 2.7 - - - +
372C PHE* 3.8 13.0 - - + -
375C LEU* 4.2 6.1 - - + -
107D ASN* 2.9 23.4 + - - -
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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