Contacts of the helix formed by residues 323 - 333 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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319H ALA 2.9 10.6 + - - +
320H PHE 3.2 14.7 + - - +
322H ALA* 1.3 76.0 - - - +
324H PRO* 1.3 73.4 - - - +
325H GLU* 2.8 34.2 + - - +
326H VAL* 3.1 12.7 + - + +
327H GLN* 3.0 24.3 + - - +
382H HIS* 2.7 26.3 + - + +
387H ARG* 3.1 20.5 + - - -
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Residues in contact with PRO 324 (chain H).
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* 4.7 7.9 - - + +
324C PRO* 3.5 30.3 - - + -
322H ALA 3.5 4.9 - - - +
323H ASP* 1.3 93.4 - - - +
325H GLU* 1.3 59.9 + - - +
327H GLN* 3.4 17.0 + - - +
328H GLU* 3.1 21.8 + - - +
331H ARG* 4.7 2.8 + - - -
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Residues in contact with GLU 325 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323H ASP* 2.8 18.7 + - - +
324H PRO* 1.3 71.8 - - - +
326H VAL* 1.3 62.3 + - - +
328H GLU* 3.3 9.5 + - + +
329H ALA* 2.9 26.9 + - - +
374H ARG* 3.2 36.7 + - - +
378H LEU* 4.0 13.2 - - + +
387H ARG* 3.3 25.4 + - - +
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Residues in contact with VAL 326 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320H PHE* 3.2 71.3 - - + +
321H ARG* 4.8 3.1 - - - -
323H ASP* 3.1 18.4 + - + +
325H GLU* 1.3 78.5 - - - +
327H GLN* 1.3 52.3 + - - +
329H ALA* 2.9 3.7 + - - +
330H LEU* 2.7 49.6 + - + +
375H LEU* 4.5 3.1 - - + -
378H LEU* 4.1 22.4 - - + -
382H HIS* 4.2 4.3 - - + -
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Residues in contact with GLN 327 (chain H).
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 4.7 0.4 + - - -
322C ALA* 3.8 15.6 + - - +
327C GLN* 2.5 47.9 + - - +
321H ARG 3.5 17.1 - - - +
322H ALA 3.4 12.1 - - - +
323H ASP 3.0 12.0 + - - +
324H PRO* 3.5 14.6 + - - +
326H VAL* 1.3 75.4 - - - +
328H GLU* 1.3 57.5 + - - +
330H LEU* 3.4 15.8 + - + +
331H ARG* 3.1 49.9 + - - +
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Residues in contact with GLU 328 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324H PRO 3.1 14.1 + - - +
325H GLU* 3.5 13.5 - - + +
327H GLN* 1.3 73.6 - - - +
329H ALA* 1.3 62.0 + - - +
331H ARG* 2.8 34.7 + - - +
332H ALA* 2.8 30.8 + - + +
374H ARG* 5.8 3.6 - - - +
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Residues in contact with ALA 329 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325H GLU 2.9 14.1 + - - +
326H VAL 2.9 7.8 + - - +
328H GLU* 1.3 76.4 - - - +
330H LEU* 1.3 59.1 + - - +
332H ALA* 3.0 9.6 + - - +
333H ALA* 2.9 30.8 + - - +
371H ALA* 5.0 2.5 - - - +
374H ARG* 4.5 10.5 - - + +
375H LEU* 3.9 27.4 - - + +
378H LEU* 3.9 16.6 - - + -
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Residues in contact with LEU 330 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147G ALA* 3.7 13.0 - - + +
321H ARG* 3.7 32.3 - - - +
326H VAL* 2.7 34.4 + - + +
327H GLN* 3.5 18.8 - - + +
329H ALA* 1.3 73.0 - - - +
331H ARG* 1.3 57.4 + - + +
333H ALA* 3.4 2.9 + - - -
334H ARG 3.1 6.4 + - - -
335H LEU* 3.0 59.7 + - + +
336H ASP* 5.0 0.7 - - - -
375H LEU* 4.0 11.9 - - + -
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Residues in contact with ARG 331 (chain H).
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* 5.3 13.5 - - - +
324H PRO 4.7 2.4 + - - -
327H GLN* 3.1 41.5 + - - +
328H GLU* 2.8 44.3 + - - +
329H ALA 3.1 0.2 - - - -
330H LEU* 1.3 74.5 - - + +
332H ALA* 1.3 65.1 + - - +
333H ALA 3.1 1.3 - - - -
334H ARG* 3.0 18.7 + - - +
336H ASP* 3.8 25.4 - - + +
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Residues in contact with ALA 332 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328H GLU* 2.8 20.3 + - + +
329H ALA* 3.0 12.3 + - - +
331H ARG* 1.3 76.7 - - - +
333H ALA* 1.3 50.4 + - - +
334H ARG* 2.8 33.1 + - - +
370H MET 4.0 3.4 - - - +
371H ALA* 4.5 14.6 - - + +
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Residues in contact with ALA 333 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107G ASN* 2.7 32.6 + - - +
329H ALA 2.9 15.3 + - - +
331H ARG 3.1 0.4 - - - -
332H ALA* 1.3 76.9 - - - +
334H ARG* 1.3 60.5 + - - +
335H LEU* 3.3 20.0 - - + -
370H MET* 3.2 26.4 - - - +
371H ALA* 4.2 3.6 - - - +
372H PHE* 4.0 13.0 - - + -
375H LEU* 4.1 7.9 - - + -
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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