Contacts of the helix formed by residues 334 - 339 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107E ASN* 3.4 15.8 - - + +
108E ASP* 2.8 43.3 + - - +
330F LEU 3.2 0.2 + - - -
331F ARG 2.9 12.2 + - - +
332F ALA 2.7 32.3 + - - -
333F ALA* 1.3 77.6 - - - +
335F LEU* 1.3 60.8 + - - +
336F ASP* 3.0 18.3 + - - +
337F GLN* 3.2 32.4 + - + +
338F LEU 3.3 8.8 + - - -
368F ARG* 4.0 18.2 + - - +
369F GLY 2.8 25.9 + - - -
370F MET* 3.3 31.0 + - - +
371F ALA* 5.3 0.2 - - - +
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Residues in contact with LEU 335 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107E ASN* 3.7 10.8 - - - +
147E ALA 3.5 28.7 - - - +
148E ALA 3.8 10.3 - - - +
149E LYS 4.3 0.2 - - - -
150E ASP* 3.8 29.9 - - + +
330F LEU* 3.0 34.6 + - + +
333F ALA* 3.6 25.8 - - + -
334F ARG* 1.3 77.3 - - - +
336F ASP* 1.3 60.3 + - - +
337F GLN 3.4 0.2 - - - -
338F LEU* 3.4 26.7 - - + +
339F ALA* 3.6 7.8 + - - +
375F LEU* 4.3 1.3 - - + -
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Residues in contact with ASP 336 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330F LEU 4.5 0.8 + - - -
331F ARG* 3.8 28.7 - - + +
334F ARG* 3.3 18.2 - - - +
335F LEU* 1.3 79.3 + - - +
337F GLN* 1.3 72.4 + - - +
338F LEU 3.1 0.2 - - - -
339F ALA* 3.1 17.8 + - - +
340F GLU* 3.3 22.0 + - - +
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Residues in contact with GLN 337 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107E ASN 3.2 12.8 - - - +
108E ASP* 3.8 7.7 + - - +
109E ARG* 2.9 36.9 - - + +
110E ASP* 4.5 2.8 + - - +
112E ARG* 2.9 23.6 + - - -
334F ARG* 3.2 30.4 + - + +
336F ASP* 1.3 81.9 - - - +
338F LEU* 1.3 62.2 + - - +
340F GLU* 3.0 29.8 + - - +
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Residues in contact with LEU 338 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105E THR 3.4 28.0 - - - +
106E ALA 4.0 7.0 - - - +
107E ASN* 3.5 24.4 + - - +
112E ARG* 3.7 6.7 - - - +
149E LYS* 3.7 9.0 - - + -
150E ASP* 3.6 37.9 - - + +
153E ALA* 4.0 12.3 - - + +
154E ALA* 4.3 11.2 - - - +
157E ARG* 2.9 39.4 + - + +
334F ARG 3.3 5.6 + - - +
335F LEU* 3.4 18.6 - - + +
336F ASP 3.1 0.4 - - - -
337F GLN* 1.3 79.9 - - - +
339F ALA* 1.3 54.8 + - - +
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Residues in contact with ALA 339 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153E ALA* 4.4 14.1 - - + -
157E ARG* 3.3 15.2 + - - +
335F LEU 3.6 7.5 + - - +
336F ASP* 3.1 12.9 + - - +
338F LEU* 1.3 77.2 - - - +
340F GLU* 1.3 58.6 + - - +
341F PRO* 4.0 4.0 - - - +
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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