Contacts of the helix formed by residues 334 - 339 (chain G) 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 ARG 334 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331G ARG 2.9 13.4 + - - +
332G ALA* 2.8 31.5 + - - +
333G ALA* 1.3 78.3 - - - +
335G LEU* 1.3 64.4 + - - +
336G ASP* 3.0 15.1 + - - +
337G GLN* 3.2 33.9 + - + +
338G LEU 3.3 8.3 + - - -
368G ARG* 4.1 17.5 - - - +
369G GLY 3.0 24.4 + - - -
370G MET* 3.0 33.4 + - - +
107H ASN* 3.4 16.7 - - + +
108H ASP* 2.8 43.1 + - - +
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Residues in contact with LEU 335 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330G LEU* 3.1 34.3 + - + +
333G ALA* 3.6 23.1 - - + -
334G ARG* 1.3 77.1 - - - +
336G ASP* 1.3 60.8 - - - +
338G LEU* 3.3 26.6 + - + +
339G ALA* 3.5 8.3 + - - +
375G LEU* 4.4 1.1 - - + -
107H ASN* 3.6 17.0 - - - +
147H ALA 3.5 22.4 - - - +
148H ALA* 3.5 22.0 - - - +
150H ASP* 4.0 21.8 - - + +
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Residues in contact with ASP 336 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330G LEU 4.5 0.8 + - - -
331G ARG* 4.0 32.1 - - + +
334G ARG* 3.2 18.7 - - - +
335G LEU* 1.3 72.6 + - - +
337G GLN* 1.3 74.8 + - - +
339G ALA* 3.2 17.2 + - - +
340G GLU* 3.4 21.5 - - - +
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Residues in contact with GLN 337 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334G ARG* 3.2 26.8 + - + +
336G ASP* 1.3 89.1 + - - +
338G LEU* 1.3 60.8 + - - +
339G ALA 3.0 2.2 - - - -
340G GLU* 2.8 38.3 + - - +
368G ARG* 5.7 1.9 + - - -
107H ASN 3.2 12.6 - - - +
108H ASP* 3.8 6.8 + - - +
109H ARG* 3.0 35.0 - - + +
110H ASP* 4.7 2.6 - - - +
112H ARG* 3.0 17.7 + - - -
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Residues in contact with LEU 338 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334G ARG 3.3 6.8 + - - +
335G LEU* 3.3 20.6 - - + +
337G GLN* 1.3 77.2 - - - +
339G ALA* 1.3 51.3 + - - +
105H THR 3.4 22.7 - - - +
106H ALA 3.8 8.5 - - - +
107H ASN* 3.2 28.9 + - - +
112H ARG* 3.6 6.3 - - - +
149H LYS* 3.9 9.2 - - + +
150H ASP* 3.8 35.9 - - + +
153H ALA* 4.1 12.3 - - + +
154H ALA* 4.5 5.4 - - - +
157H ARG* 2.7 48.7 + - + +
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Residues in contact with ALA 339 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335G LEU 3.5 6.9 + - - +
336G ASP* 3.2 13.8 + - - +
337G GLN 3.0 0.6 - - - -
338G LEU* 1.3 79.3 - - - +
340G GLU* 1.3 59.5 + - - +
341G PRO* 4.0 4.0 - - - +
153H ALA* 4.4 12.1 - - + +
157H ARG* 3.4 11.2 + - - +
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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