Contacts of the helix formed by residues 328 - 336 (chain B) in PDB entry 6EZG
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 328 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326B ASP 3.0 1.8 + - - -
327B GLU* 1.3 80.3 - - - +
329B SER* 1.3 63.4 + - - +
330B PHE 3.4 0.4 - - - -
331B PHE* 3.0 17.5 + - - +
332B LEU* 3.3 13.3 + - - +
392B ASP* 3.6 9.6 + - - -
395B VAL* 3.5 32.8 - - - +
396B GLY* 3.7 9.3 - - - -
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Residues in contact with SER 329 (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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326B ASP 3.4 8.1 + - - -
327B GLU 3.4 0.2 - - - -
328B GLY* 1.3 74.5 - - - +
330B PHE* 1.3 70.0 + - - +
331B PHE 3.1 0.7 + - - -
332B LEU* 3.3 5.7 + - - +
333B LEU* 3.2 21.7 + - - +
392B ASP* 3.2 24.3 + - - -
435B TRP* 3.9 12.9 - - - -
436B MET* 2.8 49.6 + - - +
439B ILE* 4.0 5.5 - - - +
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Residues in contact with PHE 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B GLY 4.2 6.5 - - - -
81B SER* 4.9 1.1 - - - -
84B TRP* 4.0 12.1 - + - -
327B GLU 4.5 0.6 + - - -
328B GLY 3.4 0.6 - - - -
329B SER* 1.3 82.5 + - - +
331B PHE* 1.3 75.5 + - + +
333B LEU* 3.4 4.2 - - - +
334B TYR* 3.3 45.8 - + - -
432B TRP* 3.5 29.6 - + - -
436B MET* 3.7 12.1 - - + -
439B ILE* 3.5 23.5 - - + +
440B HIS* 3.7 11.7 - - + -
442B TYR* 4.1 12.3 - + - -
603B C6K 3.7 46.8 - + + +
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Residues in contact with PHE 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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287B ILE* 4.0 15.6 - - + +
288B PHE* 3.3 64.8 - + + +
290B PHE* 4.1 9.4 - + - -
327B GLU 3.7 16.8 - - - -
328B GLY 3.0 7.5 + - - +
330B PHE* 1.3 79.2 - - + +
332B LEU* 1.3 66.7 + - - +
333B LEU 3.2 1.3 - - - -
334B TYR* 3.3 3.6 + - - +
335B GLY* 3.2 19.2 + - - -
395B VAL* 4.3 9.6 - - + -
440B HIS* 3.5 33.2 - + + -
603B C6K 3.7 46.2 - - + +
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Residues in contact with LEU 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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287B ILE* 3.6 21.1 - - + -
328B GLY 3.3 10.7 + - - +
329B SER* 3.3 8.8 + - - +
331B PHE* 1.3 76.6 - - - +
333B LEU* 1.3 65.2 + - - +
336B ALA* 2.9 45.9 + - + +
339B PHE* 3.6 32.6 - - + +
359B SER* 4.3 2.0 - - - +
391B LEU* 3.5 20.0 - - + +
392B ASP* 3.4 40.4 - - + +
395B VAL* 3.6 12.8 - - + -
435B TRP* 4.8 0.7 - - + -
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Residues in contact with LEU 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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75B PHE* 4.0 17.7 - - + -
329B SER 3.2 9.1 + - - +
330B PHE 3.4 10.3 - - - +
332B LEU* 1.3 80.2 - - - +
334B TYR* 1.3 68.7 + - + +
336B ALA 5.0 1.4 - - - +
339B PHE* 4.0 13.2 - - - +
340B SER* 3.6 14.6 - - - +
341B LYS* 3.4 32.3 - - + +
432B TRP* 3.2 41.7 - - + -
435B TRP* 4.2 10.3 - - + -
436B MET* 4.0 10.3 - - + -
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Residues in contact with TYR 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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72B ASP* 2.6 42.6 + - - -
74B GLN* 3.6 24.7 + - + -
75B PHE* 3.9 14.7 - + - -
81B SER* 3.4 16.5 - - - -
330B PHE* 3.3 39.7 - + - +
331B PHE 3.3 7.0 + - - +
332B LEU 3.2 0.4 - - - -
333B LEU* 1.3 95.6 - - + +
335B GLY* 1.3 57.7 + - - +
432B TRP* 4.3 0.2 - - - -
603B C6K 3.7 56.0 - - + +
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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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287B ILE* 3.6 24.0 - - - -
331B PHE 3.2 8.1 + - - -
334B TYR* 1.3 80.0 - - - +
336B ALA* 1.3 61.5 + - - +
337B PRO* 4.0 1.7 - - - +
358B LEU* 3.6 12.6 - - - +
603B C6K 6.1 4.7 - - - -
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Residues in contact with ALA 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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287B ILE* 4.3 4.6 - - + +
332B LEU* 2.9 32.0 + - + +
333B LEU 5.0 1.7 - - - +
334B TYR 4.0 0.2 - - - -
335B GLY* 1.3 77.1 - - - +
337B PRO* 1.3 74.0 - - + +
338B GLY 3.6 1.6 + - - -
339B PHE* 3.4 35.5 + - + +
355B GLY* 4.7 8.7 - - - -
358B LEU* 4.0 8.7 - - + -
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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