Contacts of the helix formed by residues 332 - 337 (chain B) in PDB entry 4N41
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 332 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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327B VAL* 3.6 16.0 - - + -
328B SER* 2.9 36.4 + - - -
329B LYS* 2.8 40.2 + - - +
331B ALA* 1.3 77.8 - - - +
333B ALA* 1.3 57.1 + - - +
334B LEU 3.1 0.2 - - - -
335B ARG* 3.1 8.9 + - - +
336B VAL* 2.9 32.6 + - + +
444B ARG* 5.0 3.8 + - - -
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Residues in contact with ALA 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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323B GLY* 4.7 0.4 - - - -
327B VAL* 4.0 8.3 - - + +
330B PRO 3.2 16.4 + - - +
331B ALA 3.0 1.2 - - - -
332B ASP* 1.3 73.4 - - - +
334B LEU* 1.3 57.5 + - - +
335B ARG 3.0 5.6 - - - -
336B VAL 4.2 0.2 - - - +
337B GLY* 2.8 49.6 + - - +
338B PHE* 3.9 15.5 + - + -
368B ALA* 4.7 0.5 - - - +
452B LEU* 5.5 0.7 - - + -
462B VAL* 3.9 20.9 - - + +
463B VAL* 4.6 6.5 - - + -
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Residues in contact with LEU 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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331B ALA* 3.0 15.4 + - - +
333B ALA* 1.3 77.0 - - - +
335B ARG* 1.3 68.5 + - + +
338B PHE* 4.2 6.7 - - + -
364B ALA* 4.1 10.1 - - + +
365B LEU* 5.9 1.3 - - + -
367B ARG* 4.1 2.8 - - - +
368B ALA* 3.2 36.5 + - + +
447B TRP* 5.2 1.1 - - + -
448B GLU* 3.8 50.9 - - + +
451B LEU* 4.5 17.3 - - + -
452B LEU* 4.2 15.7 - - + -
455B LEU* 4.0 28.0 - - + -
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Residues in contact with ARG 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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331B ALA 4.9 6.4 + - - +
332B ASP* 3.1 8.7 + - - +
333B ALA 3.0 0.2 - - - -
334B LEU* 1.3 87.7 - - + +
336B VAL* 1.3 65.7 + - + +
337B GLY 3.3 1.3 - - - -
363B ARG* 6.0 1.8 - - - +
364B ALA* 6.3 0.4 - - - +
367B ARG* 4.7 7.8 - - + +
368B ALA* 5.3 0.2 - - - +
371B ALA* 3.3 17.4 - - - +
444B ARG* 3.8 28.0 - - - +
447B TRP* 5.4 7.7 - - - -
448B GLU* 2.9 30.3 + - - -
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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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324B ARG* 3.5 9.2 - - - +
325B ARG* 3.4 47.1 - - + +
326B ALA 4.3 11.0 - - - +
327B VAL* 4.4 5.2 - - + -
332B ASP* 2.9 24.5 + - + +
333B ALA* 4.5 0.2 - - - -
335B ARG* 1.3 78.6 - - + +
337B GLY* 1.3 60.3 + - - +
371B ALA* 3.5 11.6 - - - +
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Residues in contact with GLY 337 (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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323B GLY* 3.5 1.4 - - - -
324B ARG* 2.7 26.8 + - - -
333B ALA* 2.8 30.4 + - - +
335B ARG 3.3 1.6 - - - -
336B VAL* 1.3 79.7 - - - +
338B PHE* 1.3 60.8 + - - -
368B ALA 4.3 0.9 - - - -
371B ALA* 4.0 8.5 - - - -
372B SER* 3.3 13.7 - - - -
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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