Contacts of the helix formed by residues 329 - 337 (chain A) in PDB entry 5M8N
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 GLU 329 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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252A ALA* 3.6 8.0 - - - +
254A GLY* 4.0 9.2 - - - +
326A ARG* 5.4 9.5 - - - +
327A LEU 4.5 8.0 - - - +
328A PRO* 1.3 76.8 - - - +
330A PRO* 1.3 71.7 - - + +
331A GLN* 2.8 22.9 - - - +
332A ASP* 2.7 56.5 + - - +
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Residues in contact with PRO 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252A ALA* 3.2 24.2 - - + +
253A THR* 4.3 13.2 - - - +
254A GLY* 4.9 0.7 - - - -
329A GLU* 1.3 84.5 - - + +
331A GLN* 1.3 83.8 + - - +
333A VAL* 3.2 9.5 + - + +
334A ALA 3.2 15.4 + - - -
469A PRO* 3.6 17.6 - - + +
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Residues in contact with GLN 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329A GLU* 2.8 28.9 - - - +
330A PRO* 1.3 89.5 - - - +
332A ASP* 1.3 57.2 + - - +
334A ALA* 3.4 10.8 - - + +
335A GLN* 2.7 49.8 + - + +
469A PRO* 5.7 0.4 - - - -
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Residues in contact with ASP 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328A PRO* 3.4 8.8 - - - +
329A GLU* 2.7 58.1 + - - +
331A GLN* 1.3 75.1 - - - +
333A VAL* 1.3 60.5 + - - +
335A GLN* 3.1 3.8 + - - +
336A CYS* 2.8 32.6 + - - +
365A PRO* 3.3 34.7 - - + +
375A SER* 5.6 1.6 - - - -
376A LEU* 3.7 19.8 + - + +
379A LEU* 5.2 2.1 - - - +
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Residues in contact with VAL 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252A ALA* 3.6 27.4 - - + -
329A GLU 3.8 0.6 + - - -
330A PRO* 3.2 9.6 + - + +
332A ASP* 1.3 76.3 - - - +
334A ALA* 1.3 65.7 + - - +
336A CYS* 3.7 4.5 - - - -
337A LEU* 3.2 27.8 + - + +
376A LEU* 3.9 15.9 - - + -
406A PHE* 4.0 19.5 - - + -
410A VAL* 4.7 7.6 - - + -
468A TRP* 3.4 37.0 - - + -
469A PRO* 4.4 8.5 - - + -
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Residues in contact with ALA 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330A PRO 3.2 4.2 + - - -
331A GLN* 3.4 17.0 - - + +
332A ASP 3.2 0.2 - - - -
333A VAL* 1.3 82.4 - - - +
335A GLN* 1.3 63.8 + - + +
337A LEU* 3.3 10.7 + - - +
338A GLU* 3.4 24.7 + - - +
417A ARG* 6.2 0.9 - - - +
469A PRO* 3.5 31.8 - - + +
470A SER 5.1 6.7 - - - +
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Residues in contact with GLN 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331A GLN* 2.7 32.3 + - + +
332A ASP* 3.8 4.4 - - - +
334A ALA* 1.3 74.2 - - + +
336A CYS* 1.3 66.2 + - - +
338A GLU* 2.9 23.1 + - + +
339A VAL* 3.6 5.7 + - - +
365A PRO* 3.3 34.4 - - + +
366A THR* 4.0 24.1 - - + +
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Residues in contact with CYS 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332A ASP 2.8 17.2 + - - +
333A VAL* 3.7 14.1 - - - -
335A GLN* 1.3 73.3 - - - +
337A LEU* 1.3 61.1 + - - +
339A VAL* 3.2 20.7 + - - +
355A PHE* 3.3 27.8 - - + -
358A THR* 3.6 24.7 - - + -
359A VAL* 4.2 10.5 - - - +
365A PRO 3.2 9.1 + - - -
376A LEU* 4.2 9.2 - - + -
410A VAL* 3.9 27.1 - - - -
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Residues in contact with LEU 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333A VAL* 3.2 23.8 + - + +
334A ALA* 3.7 4.7 - - - +
335A GLN 3.0 1.4 - - - -
336A CYS* 1.3 77.7 - - - +
338A GLU* 1.3 48.5 + - - +
339A VAL 3.4 0.4 - - - -
355A PHE* 4.6 3.6 - - + -
410A VAL* 3.8 17.7 - - + +
413A GLU* 3.6 27.4 - - + -
414A TRP* 3.6 39.5 - - + +
417A ARG* 3.3 33.1 + - - +
418A TYR* 2.7 30.9 + - - -
468A TRP* 3.9 26.0 - - + -
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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