Contacts of the helix formed by residues 327 - 335 (chain E) in PDB entry 3G76
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 CYS 327 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300E CYS* 3.9 3.4 - - - -
302E HIS* 4.0 6.3 - - - -
303E CYS* 3.8 12.7 - - + +
320E HIS* 3.5 9.6 - - - +
324E TYR* 3.3 12.7 + - - +
325E PRO 3.6 1.1 - - - +
326E GLY* 1.3 74.8 - - - +
328E LYS* 1.3 58.3 - - - +
329E TYR* 3.4 16.6 - - - -
330E LEU* 3.1 28.6 + - + +
331E LEU* 2.9 26.7 + - - +
502E ZN 2.5 35.7 - - - -
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Residues in contact with LYS 328 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254E THR* 5.0 14.3 - - + +
255E ASN* 4.3 23.1 + - + +
302E HIS* 3.5 24.9 - - + +
326E GLY 3.2 6.9 + - - +
327E CYS* 1.3 70.3 - - - +
329E TYR* 1.3 54.5 + - - +
331E LEU* 3.8 29.4 - - + -
332E GLU* 2.6 59.2 + - + +
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Residues in contact with TYR 329 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268E ARG* 3.5 11.3 + - - -
286E ARG 2.8 19.6 + - - -
287E ALA 3.4 31.4 - - - -
288E GLY* 3.8 2.7 - - - -
300E CYS* 5.2 0.4 - - - -
301E PHE* 3.4 32.3 - + - -
302E HIS* 3.8 24.4 + + + -
317E TRP* 3.7 5.6 - + - -
320E HIS* 4.8 1.1 - + - -
327E CYS* 3.2 14.4 - - - -
328E LYS* 1.3 76.8 - - - +
330E LEU* 1.3 58.1 + - - +
332E GLU* 2.9 13.5 + - - +
333E GLN* 2.7 82.1 + - + +
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Residues in contact with LEU 330 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317E TRP* 4.4 19.7 - - + -
320E HIS* 4.1 11.0 - - + +
321E ALA* 3.7 33.4 - - + +
324E TYR 3.4 25.1 - - - +
325E PRO 4.2 4.7 - - - +
327E CYS* 3.1 20.5 - - + +
329E TYR* 1.3 80.4 - - - +
331E LEU* 1.3 57.1 + - - +
333E GLN 3.3 0.2 + - - -
334E LYS* 2.8 54.6 + - + +
338E TYR* 4.4 3.6 - - + -
339E ILE* 3.8 29.6 - - + -
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Residues in contact with LEU 331 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326E GLY 5.8 1.1 - - - +
327E CYS 2.9 13.8 + - - +
328E LYS* 3.4 33.0 - - + +
330E LEU* 1.3 75.7 - - - +
332E GLU* 1.3 59.3 + - - +
335E GLY* 2.9 25.9 + - - +
336E GLN* 3.4 50.5 - - + +
339E ILE* 4.2 11.2 - - + -
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Residues in contact with GLU 332 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328E LYS* 2.6 40.1 + - - +
329E TYR* 3.2 16.0 - - - +
331E LEU* 1.3 76.5 - - - +
333E GLN* 1.3 81.0 + - - +
334E LYS 3.5 0.3 + - - -
335E GLY 4.7 0.5 + - - -
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Residues in contact with GLN 333 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317E TRP* 3.7 22.5 - - + -
329E TYR* 2.7 65.7 + - + +
330E LEU 4.2 0.4 - - - +
332E GLU* 1.3 93.7 + - - +
334E LYS* 1.3 65.1 + - - +
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Residues in contact with LYS 334 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286E ARG* 5.7 0.2 - - - +
317E TRP* 3.7 59.4 - - + +
330E LEU* 2.8 26.4 + - + +
333E GLN* 1.3 89.9 - - - +
335E GLY* 1.3 63.4 + - - +
338E TYR* 3.3 59.3 + - + +
339E ILE* 5.3 0.7 - - + -
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Residues in contact with GLY 335 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331E LEU* 2.9 22.7 + - - -
332E GLU 4.7 1.0 + - - -
334E LYS* 1.3 79.1 - - - +
336E GLN* 1.3 60.1 + - - -
337E GLU 3.2 2.9 - - - -
338E TYR* 2.9 24.5 + - - +
339E ILE* 3.5 5.4 + - - +
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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