Contacts of the helix formed by residues 334 - 340 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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330E LEU 3.1 0.2 + - - -
331E ARG 3.0 11.4 + - - +
332E ALA 2.8 31.4 + - - -
333E ALA* 1.3 79.5 - - - +
335E LEU* 1.3 64.2 + - - +
336E ASP* 3.0 13.7 - - - +
337E GLN* 3.2 28.3 + - + +
338E LEU 3.2 9.0 + - - -
368E ARG* 3.3 49.3 - - - +
369E GLY 2.7 21.6 + - - -
370E MET* 3.0 30.2 - - - +
107F ASN* 3.5 21.6 - - + +
108F ASP* 2.6 43.7 + - - +
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Residues in contact with LEU 335 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330E LEU* 3.1 32.7 + - + +
333E ALA* 3.5 23.6 - - + -
334E ARG* 1.3 76.5 - - - +
336E ASP* 1.3 62.0 + - - +
337E GLN 3.4 0.2 - - - -
338E LEU* 3.4 37.8 - - + +
339E ALA* 3.6 7.3 + - - +
375E LEU* 4.4 0.4 - - + -
107F ASN* 3.5 14.6 - - - +
147F ALA 3.5 20.2 - - - +
148F ALA* 3.3 25.8 - - - +
150F ASP* 3.9 12.1 - - + +
153F ALA* 5.9 0.3 - - - +
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Residues in contact with ASP 336 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330E LEU 4.5 1.0 + - - -
331E ARG* 3.7 30.0 - - + +
334E ARG* 3.3 18.5 - - - +
335E LEU* 1.3 74.4 + - - +
337E GLN* 1.3 71.0 + - - +
339E ALA* 3.3 16.1 + - - +
340E GLU* 3.5 18.3 + - - +
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Residues in contact with GLN 337 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334E ARG* 3.2 27.1 + - + +
336E ASP* 1.3 85.7 - - - +
338E LEU* 1.3 62.5 + - - +
339E ALA 3.1 2.2 - - - -
340E GLU* 2.9 33.6 + - - +
368E ARG* 5.7 1.0 + - - -
107F ASN 3.2 12.3 - - - +
108F ASP* 3.6 8.6 + - - +
109F ARG* 2.8 41.9 - - + +
110F ASP* 4.5 2.8 + - - +
112F ARG* 2.9 23.7 + - - -
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Residues in contact with LEU 338 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334E ARG 3.2 8.5 + - - +
335E LEU* 3.4 21.3 - - + +
336E ASP 3.2 0.2 - - - -
337E GLN* 1.3 76.6 - - - +
339E ALA* 1.3 56.7 + - - +
105F THR 3.7 18.8 - - - +
106F ALA 4.2 6.5 - - - +
107F ASN* 3.5 32.3 + - - +
112F ARG* 4.0 2.2 - - - +
149F LYS* 3.7 9.4 - - + -
150F ASP* 3.6 35.9 - - + +
153F ALA* 4.0 12.7 - - + +
154F ALA* 4.1 14.4 - - - -
157F ARG* 2.9 40.1 + - + +
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Residues in contact with ALA 339 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335E LEU 3.6 6.0 + - - +
336E ASP* 3.3 12.3 + - - +
338E LEU* 1.3 75.5 - - - +
340E GLU* 1.3 61.7 + - - +
341E PRO* 3.8 3.8 - - - +
153F ALA* 4.4 13.0 - - + +
157F ARG* 2.9 17.7 + - - +
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Residues in contact with GLU 340 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336E ASP* 3.6 17.1 - - - +
337E GLN* 2.9 35.2 + - - +
339E ALA* 1.3 78.0 - - - +
341E PRO* 1.3 72.0 - - + +
109F ARG* 4.1 16.5 + - - -
112F ARG* 2.8 25.2 + - - +
157F ARG* 3.2 10.9 - - - -
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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