Contacts of the helix formed by residues 319 - 326 (chain E) in PDB entry 6CP3
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 319 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279E VAL* 4.2 12.0 - - - +
281E TYR* 3.2 33.0 + - - -
313E PRO* 3.3 23.5 - - + +
316E ASP* 4.3 11.0 + - + +
317E LEU 3.6 0.2 - - - -
318E THR* 1.3 75.6 - - - +
320E PRO* 1.3 79.5 - - - +
321E ALA 3.0 1.9 + - - -
322E PRO* 3.2 14.5 - - + +
323E ALA* 3.0 17.5 + - - +
259G ARG* 4.4 17.5 + - - +
260G GLN* 3.2 11.9 - - - +
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Residues in contact with PRO 320 (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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281B ARG* 5.3 11.4 - - - +
278E ALA* 5.8 3.1 - - + -
279E VAL* 3.8 26.7 - - + +
281E TYR* 4.3 7.2 - - + -
285E LEU* 3.8 17.8 - - + +
318E THR 3.5 7.6 - - - +
319E ASP* 1.3 92.2 - - - +
321E ALA* 1.3 56.8 + - - +
323E ALA* 3.7 11.0 - - + -
324E THR* 2.4 36.0 + - - +
260G GLN* 4.3 2.5 - - - +
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Residues in contact with ALA 321 (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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259E PHE* 4.0 15.7 - - + -
262E THR* 3.8 27.4 - - + +
281E TYR* 3.6 27.2 - - + -
285E LEU* 4.9 2.0 - - - -
289E MET* 5.1 2.1 - - - +
319E ASP 3.0 2.0 + - - -
320E PRO* 1.3 75.4 - - - +
322E PRO* 1.3 66.7 - - + +
324E THR* 3.3 3.5 + - - -
325E THR* 3.0 32.2 + - - -
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Residues in contact with PRO 322 (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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259E PHE* 5.3 1.3 - - + -
310E VAL* 4.7 13.0 - - + -
311E TYR 5.5 0.4 - - - +
312E VAL* 4.9 0.4 - - + -
313E PRO* 3.6 33.9 - - + -
316E ASP 3.8 14.4 - - - +
317E LEU* 4.0 22.0 - - + -
319E ASP* 3.2 18.6 - - + +
321E ALA* 1.3 88.0 - - + +
323E ALA* 1.3 54.4 + - - -
324E THR 3.1 0.7 - - - -
325E THR* 4.3 6.7 - - - +
326E PHE* 2.9 45.7 + - + -
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Residues in contact with ALA 323 (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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173B ARG* 4.9 9.7 + - - +
275B LYS* 5.7 0.7 + - - -
330B GLU* 5.1 6.4 - - - +
332B GLN* 3.4 33.8 - - - +
317E LEU 4.4 6.2 + - - +
318E THR 4.3 2.0 - - - +
319E ASP 3.0 19.0 + - - +
320E PRO* 3.6 9.9 - - + -
322E PRO* 1.3 76.8 - - - +
324E THR* 1.3 58.3 + - - +
326E PHE* 4.3 6.5 - - - +
327E ALA* 4.3 11.3 + - - +
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Residues in contact with THR 324 (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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275B LYS* 5.5 7.4 - - - +
285E LEU* 3.4 25.4 - - + +
286E ALA* 4.6 12.8 - - + -
289E MET* 4.3 26.5 - - + -
320E PRO* 2.4 27.0 + - - +
321E ALA* 3.9 3.1 - - - -
323E ALA* 1.3 78.0 - - - +
325E THR* 1.3 64.9 + - - +
326E PHE 3.2 1.6 - - - -
327E ALA* 3.3 9.9 + - - +
328E HIS* 3.2 27.9 - - + +
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Residues in contact with THR 325 (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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258E ILE* 4.0 21.6 - - + +
262E THR* 5.2 0.9 + - - -
289E MET* 4.1 17.7 - - - +
293E GLN* 5.9 1.8 - - - +
308E GLN* 4.5 12.1 - - + +
310E VAL* 4.2 15.5 - - + -
321E ALA 3.0 18.6 + - - -
322E PRO* 4.0 6.2 - - - +
324E THR* 1.3 75.4 - - - +
326E PHE* 1.3 58.5 + - - +
328E HIS* 2.9 24.6 + - + +
329E LEU* 3.2 33.7 + - + +
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Residues in contact with PHE 326 (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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173B ARG* 3.3 51.6 - - - +
174B GLN* 3.9 15.9 + - - +
156E PHE* 3.4 39.5 - + - -
310E VAL* 4.5 10.3 - - + -
312E VAL* 5.0 0.9 - - + -
317E LEU* 3.6 38.8 - - + -
322E PRO* 2.9 28.1 + - + +
323E ALA* 4.7 1.6 - - - -
324E THR 3.2 0.4 - - - -
325E THR* 1.3 74.6 - - + +
327E ALA* 1.3 56.8 + - - +
328E HIS 3.2 5.1 + - - -
329E LEU* 3.6 28.3 + - + +
332E THR* 5.1 4.3 - - + -
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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