Contacts of the helix formed by residues 329 - 336 (chain B) in PDB entry 4M3P
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 GLY 329 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40A LYS* 5.1 1.1 - - - -
312B GLU* 4.2 0.7 - - - +
328B HIS* 1.3 100.6 + - - +
330B SER* 1.3 65.3 + - - -
331B TRP 3.3 2.8 + - - -
332B GLY* 4.2 2.2 + - - -
333B SER* 3.1 19.1 - - - -
334B GLY 4.4 7.5 - - - +
398C PHE* 3.6 15.9 - - - -
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Residues in contact with SER 330 (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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312B GLU* 5.4 0.9 - - - -
329B GLY* 1.3 69.5 - - - -
331B TRP* 1.3 88.3 + - - +
333B SER* 2.9 23.1 + - - -
347B ALA 4.8 0.9 - - - +
395C LYS* 4.8 16.5 + - - +
398C PHE* 3.7 33.0 - - - +
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Residues in contact with TRP 331 (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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279B TRP* 3.4 62.5 - + + -
282B GLN* 3.3 41.8 + - + +
283B LYS 5.6 0.7 - - - -
312B GLU* 5.5 1.0 + - - -
313B GLU* 4.0 9.4 + - - -
329B GLY 3.3 4.0 + - - -
330B SER* 1.3 92.3 + - - +
332B GLY* 1.3 58.6 + - - +
347B ALA 3.5 0.2 - - - -
348B ARG* 3.4 25.4 + - - +
349B LYS* 3.6 68.5 - - + +
352B TRP* 4.0 8.5 - - + -
353B GLU* 4.2 23.1 - - + -
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Residues in contact with GLY 332 (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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269A PHE* 3.9 24.2 - - - -
279B TRP* 3.7 8.5 - - - -
328B HIS* 5.5 0.8 + - - -
329B GLY* 4.2 3.8 + - - -
330B SER 3.2 0.6 - - - -
331B TRP* 1.3 74.4 - - - +
333B SER* 1.3 64.9 + - - +
334B GLY* 3.0 5.0 + - - -
335B LEU* 3.0 16.5 + - - +
346B ARG 4.3 0.7 - - - -
347B ALA* 3.3 15.4 - - - -
352B TRP* 4.2 11.7 - - - -
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Residues in contact with SER 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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40A LYS* 5.7 1.0 + - - -
329B GLY* 3.1 25.4 - - - -
330B SER* 2.9 21.0 + - - -
331B TRP 3.4 0.6 + - - -
332B GLY* 1.3 75.9 - - - +
334B GLY* 1.3 61.8 + - - +
335B LEU 3.1 0.5 + - - -
336B ASP* 3.0 35.2 + - - +
347B ALA* 4.0 13.5 - - - -
398C PHE* 5.6 0.3 - - - +
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Residues in contact with GLY 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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40A LYS* 4.2 19.7 - - - -
41A ALA 3.9 18.1 - - - +
42A GLY* 3.6 16.3 - - - -
43A PRO* 4.6 3.3 - - - +
269A PHE* 5.9 2.9 - - - -
329B GLY* 4.4 5.5 - - - -
332B GLY 3.0 2.2 + - - -
333B SER* 1.3 79.1 + - - +
335B LEU* 1.3 59.1 + - - +
336B ASP* 3.3 2.5 + - - +
337B MET* 4.4 7.1 + - - +
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Residues in contact with LEU 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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41A ALA* 5.0 0.4 - - + -
42A GLY* 4.8 16.4 - - - +
44A TRP* 5.9 1.1 - - - +
267A PHE* 4.5 4.3 - - + +
268A PRO* 3.8 39.3 - - + -
269A PHE* 4.0 17.9 - - + -
332B GLY 3.0 15.0 + - - +
334B GLY* 1.3 76.4 - - - +
336B ASP* 1.3 56.6 + - - +
337B MET 2.9 12.8 + - - -
338B HIS* 3.0 25.9 + - + +
343B VAL* 4.0 26.2 - - + +
344B ARG* 3.8 5.6 - - - +
346B ARG* 3.8 28.3 - - + -
347B ALA* 4.4 3.6 - - + -
352B TRP* 4.2 4.5 - - + +
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Residues in contact with ASP 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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333B SER* 3.0 27.5 + - - +
334B GLY 3.3 2.1 - - - +
335B LEU* 1.3 75.0 - - - +
337B MET* 1.3 89.4 + - - +
338B HIS 3.5 0.7 - - - -
344B ARG* 3.1 24.7 - - + +
347B ALA* 3.8 19.3 - - + +
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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