Contacts of the helix formed by residues 332 - 336 (chain B) in PDB entry 1F6A
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 ASN 332 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117A LYS* 5.9 0.4 - - - +
371A CPS 5.7 2.1 - - - -
329B CYS* 3.9 13.8 + - - +
330B ASP 3.7 0.2 - - - -
331B SER* 1.3 106.1 + - - +
333B PRO* 1.3 71.9 - - - +
334B ARG 3.2 0.5 + - - -
335B GLY* 2.6 24.4 + - - -
336B VAL 3.7 8.1 - - - +
337B SER* 3.6 28.0 - - - +
427B ARG* 4.2 7.5 + - - -
431B ARG* 4.3 4.7 + - - -
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Residues in contact with PRO 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331B SER* 3.3 4.0 - - - -
332B ASN* 1.3 87.2 - - - +
334B ARG* 1.3 56.8 + - - +
335B GLY 2.3 15.8 + - - -
336B VAL* 2.6 21.6 + - - +
425B LEU* 4.0 20.0 - - + -
426B PRO* 4.2 3.6 - - + -
427B ARG* 3.3 54.9 - - + +
428B ALA 3.6 10.1 - - - +
429B LEU* 3.3 25.8 - - + -
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Residues in contact with ARG 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A LYS* 5.3 1.4 - - - -
130A TRP* 3.4 17.9 - - - -
131A TYR* 3.2 46.4 - - + +
132A GLU* 2.4 50.9 + - - +
371A CPS 5.6 12.9 - - - -
201B SO4 2.6 34.9 + - - -
332B ASN 3.2 0.4 + - - -
333B PRO* 1.3 70.3 - - - +
335B GLY* 1.3 56.3 + - - +
336B VAL 3.3 2.3 + - - -
424B HIS* 3.1 30.6 + - - +
425B LEU* 3.7 16.8 - - + -
426B PRO* 4.2 10.8 - - + +
427B ARG* 3.9 10.3 - - - +
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Residues in contact with GLY 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A LYS* 3.2 33.7 + - - -
131A TYR* 5.5 0.4 - - - -
371A CPS 4.8 17.6 - - - -
332B ASN* 2.6 25.6 + - - -
333B PRO 2.3 12.3 + - - -
334B ARG* 1.3 71.0 - - - +
336B VAL* 1.3 61.3 + - - -
337B SER* 3.1 5.7 + - - -
362B ASP* 4.3 1.1 - - - +
427B ARG* 5.3 0.4 - - - +
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Residues in contact with VAL 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A TYR* 3.3 35.9 - - + -
332B ASN* 3.7 7.0 - - - -
333B PRO 2.6 19.4 + - - +
335B GLY* 1.3 69.1 - - - +
337B SER* 1.3 57.8 + - - +
360B VAL* 3.8 22.4 - - + -
361B VAL 3.5 16.6 - - - +
362B ASP* 3.8 11.0 - - - +
363B LEU* 3.9 13.7 - - + -
420B VAL* 5.5 0.7 - - + -
425B LEU* 4.1 18.2 - - + -
429B LEU* 3.0 27.4 - - + +
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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