Contacts of the helix formed by residues 319 - 326 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293B ARG* 2.5 32.2 + - - +
259F PHE* 4.0 2.4 - - - -
279F VAL* 5.7 0.2 - - - -
281F TYR* 2.9 35.5 + - - -
313F PRO* 3.8 16.7 - - + +
316F ASP* 2.8 18.8 + - - +
317F LEU 3.2 0.8 - - - +
318F THR* 1.3 79.9 - - - +
320F PRO* 1.3 73.0 - - - +
321F ALA 3.3 4.3 + - - -
322F PRO* 3.3 24.0 - - + +
323F ALA* 3.2 20.6 + - - +
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Residues in contact with PRO 320 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281C ARG* 5.6 9.2 - - - +
278F ALA* 4.9 7.6 - - + -
279F VAL* 3.8 28.0 - - + +
281F TYR* 3.7 23.6 - - + -
285F LEU* 4.8 9.6 - - + -
318F THR 3.9 6.7 - - - +
319F ASP* 1.3 96.2 - - - +
321F ALA* 1.3 52.7 + - - +
323F ALA* 3.9 4.6 - - + +
324F THR* 2.4 39.9 + - - +
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Residues in contact with ALA 321 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259F PHE* 3.7 27.4 - - + -
262F THR* 4.0 25.6 - - + +
281F TYR* 5.0 4.9 - - + -
285F LEU* 4.5 8.7 - - + +
289F MET* 4.2 3.5 - - + +
319F ASP* 3.3 3.6 + - - +
320F PRO* 1.3 78.4 - - - +
322F PRO* 1.4 60.4 - - + +
324F THR* 3.2 7.0 + - - -
325F THR* 2.6 35.4 + - - -
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Residues in contact with PRO 322 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156F PHE* 3.4 20.4 - - + -
259F PHE* 4.7 7.4 - - + -
310F VAL* 3.8 14.6 - - + -
312F VAL* 4.0 22.2 - - + -
313F PRO* 4.9 0.7 - - + -
316F ASP 5.0 0.4 - - - +
317F LEU* 5.0 6.1 - - + +
319F ASP* 3.3 33.7 - - + +
321F ALA* 1.4 89.1 - - + +
323F ALA* 1.3 57.3 + - - +
325F THR* 3.0 10.7 + - - +
326F PHE* 3.0 37.6 + - + -
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Residues in contact with ALA 323 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173C ARG* 5.6 1.3 - - - +
275C LYS* 5.8 1.4 - - - -
330C GLU* 3.9 14.1 - - - +
332C GLN* 3.4 33.7 - - - +
317F LEU 4.0 6.6 + - - +
319F ASP 3.2 20.9 + - - +
320F PRO* 4.0 4.7 - - + +
322F PRO* 1.3 79.6 - - - +
324F THR* 1.3 61.9 + - - +
326F PHE* 3.7 21.2 + - - +
327F ALA* 4.5 1.6 + - - +
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Residues in contact with THR 324 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275C LYS* 5.3 12.7 - - + +
278C VAL* 6.0 2.4 - - + +
285F LEU* 3.5 26.5 - - + +
286F ALA* 4.5 19.5 - - + -
289F MET* 4.6 12.1 - - + -
320F PRO* 2.4 26.2 + - - +
321F ALA 3.5 4.5 - - - -
322F PRO 3.2 0.2 - - - -
323F ALA* 1.3 76.5 - - - +
325F THR* 1.3 63.9 + - - +
326F PHE 3.4 0.5 + - - -
327F ALA* 3.6 9.2 + - - +
328F HIS* 3.2 20.0 - - - +
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Residues in contact with THR 325 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156F PHE* 4.1 3.4 - - + -
258F ILE* 4.7 8.4 - - + +
289F MET* 3.4 21.2 - - + +
293F GLN* 5.0 12.3 - - - +
308F GLN* 5.2 0.9 - - - +
310F VAL* 3.8 21.8 - - + +
321F ALA 2.6 21.7 + - - -
322F PRO* 3.0 13.1 + - - +
324F THR* 1.3 77.7 - - - +
326F PHE* 1.3 63.1 + - - +
328F HIS* 3.0 22.1 + - - +
329F LEU* 3.6 26.7 - - + +
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Residues in contact with PHE 326 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173C ARG* 3.2 59.7 - - + -
174C GLN* 3.8 21.3 + - + +
330C GLU* 4.8 1.8 - - - +
156F PHE* 3.4 49.3 - + + -
317F LEU* 4.7 19.3 - - + -
322F PRO* 3.0 28.2 + - + -
323F ALA* 3.8 13.2 - - + +
324F THR 3.2 0.6 - - - -
325F THR* 1.3 76.1 - - - +
327F ALA* 1.3 61.5 + - - +
328F HIS 3.3 0.9 + - - -
329F LEU* 3.6 11.7 + - - +
332F THR* 3.6 22.7 - - + +
334F VAL* 4.5 8.7 - - + -
352F ASP* 4.4 3.6 - - - -
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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