Contacts of the helix formed by residues 300 - 311 (chain F) in PDB entry 5I4V
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 PRO 300 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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297F GLU* 4.0 21.1 - - + +
298F GLU* 3.4 8.3 - - - +
299F MET* 1.3 87.1 - - - +
301F VAL* 1.3 64.1 + - - +
302F ASP* 3.2 24.3 + - - +
303F ARG* 3.3 26.3 + - + +
304F ILE* 3.5 14.1 + - - +
358F PRO* 3.9 15.9 - - + -
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Residues in contact with VAL 301 (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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299F MET 3.3 1.4 + - - -
300F PRO* 1.3 69.4 - - - +
302F ASP* 1.3 70.5 + - + +
304F ILE* 3.4 9.9 + - + +
305F LEU* 3.0 22.9 + - - +
436F THR* 3.9 14.6 - - + +
440F CYS* 4.1 15.5 - - - -
470F SER* 3.6 39.0 - - - +
474F TYR* 4.1 28.5 - - + -
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Residues in contact with ASP 302 (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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300F PRO* 3.2 20.8 - - - +
301F VAL* 1.3 83.7 + - + +
303F ARG* 1.3 70.2 + - - +
305F LEU* 3.1 12.1 + - - +
306F GLU* 3.0 42.5 + - + +
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Residues in contact with ARG 303 (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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300F PRO* 3.3 23.5 + - + +
302F ASP* 1.3 92.7 - - - +
304F ILE* 1.3 61.7 + - - +
306F GLU* 3.3 18.3 + - - +
307F ALA* 3.2 20.1 + - - +
355F LYS 4.9 3.0 + - - -
356F ARG* 3.7 28.9 + - - +
357F ILE 4.6 1.0 + - - -
358F PRO* 3.8 41.4 - - + +
359F HIS* 4.8 4.0 - - - +
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Residues in contact with ILE 304 (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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299F MET* 4.0 26.5 - - + +
300F PRO 3.5 14.0 + - - +
301F VAL* 3.4 11.6 + - + +
302F ASP 3.2 0.4 - - - -
303F ARG* 1.3 74.2 - - - +
305F LEU* 1.3 66.0 + - - +
307F ALA* 3.1 17.0 + - - +
308F GLU* 3.3 12.1 + - - +
353F TRP* 4.8 0.2 + - - -
357F ILE* 4.3 13.7 - - + -
358F PRO* 4.2 15.5 - - + -
436F THR 4.3 2.9 - - - +
439F GLY* 3.4 37.0 - - - +
440F CYS* 3.6 24.0 - - - +
443F ALA* 4.6 10.5 - - + -
467F VAL* 4.9 2.9 - - + -
470F SER* 5.7 0.9 - - - -
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Residues in contact with LEU 305 (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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301F VAL 3.0 13.5 + - - +
302F ASP* 3.1 13.9 + - + +
304F ILE* 1.3 77.9 - - - +
306F GLU* 1.3 62.7 + - + +
308F GLU* 3.3 5.8 + - + +
309F LEU* 3.1 44.4 + - + +
435F LYS* 3.8 28.3 - - + -
436F THR* 3.5 31.4 - - - +
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Residues in contact with GLU 306 (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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302F ASP* 3.0 30.6 + - + +
303F ARG* 3.5 21.3 - - - +
304F ILE 3.2 0.2 - - - -
305F LEU* 1.3 77.1 - - + +
307F ALA* 1.3 52.9 + - - +
309F LEU* 3.3 9.6 + - + +
310F ALA* 2.7 38.9 + - + +
356F ARG* 5.2 2.0 - - + +
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Residues in contact with ALA 307 (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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303F ARG 3.2 7.8 + - - +
304F ILE 3.1 11.1 + - - +
306F GLU* 1.3 81.3 - - - +
308F GLU* 1.3 61.4 + - - +
310F ALA* 3.6 1.7 + - - +
311F VAL* 3.5 18.7 + - - +
353F TRP* 3.4 31.3 - - + +
356F ARG* 3.5 34.8 - - + +
357F ILE* 4.2 9.4 - - + -
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Residues in contact with GLU 308 (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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304F ILE 3.3 7.8 + - - +
305F LEU* 3.3 8.7 + - - +
307F ALA* 1.3 75.9 - - - +
309F LEU* 1.3 61.2 + - + +
311F VAL* 3.0 24.4 - - - +
312F GLU 3.3 10.6 - - - +
353F TRP* 2.6 15.7 + - - +
383F SER* 5.3 1.9 - - - -
435F LYS* 4.1 26.0 + - + +
438F LEU* 3.3 24.6 - - - +
439F GLY* 3.7 25.9 - - - -
442F ARG* 2.5 37.8 + - - -
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Residues in contact with LEU 309 (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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305F LEU* 3.1 41.8 + - + +
306F GLU* 3.8 8.1 - - + +
308F GLU* 1.3 71.5 - - - +
310F ALA* 1.3 58.3 + - - +
311F VAL 3.0 4.9 - - - -
312F GLU* 2.8 28.4 + - - +
435F LYS* 4.0 32.5 - - + +
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Residues in contact with ALA 310 (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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306F GLU* 2.7 23.4 + - + +
307F ALA 3.8 1.8 - - - +
308F GLU 3.4 0.2 - - - -
309F LEU* 1.3 71.7 - - - +
311F VAL* 1.3 60.0 + - + +
312F GLU* 3.3 3.8 + - - +
356F ARG* 3.6 40.3 + - - +
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Residues in contact with VAL 311 (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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307F ALA 3.5 13.2 + - - +
308F GLU* 3.0 24.2 - - - +
309F LEU 3.0 1.2 + - - -
310F ALA* 1.3 81.9 - - + +
312F GLU* 1.3 72.5 + - - +
346F GLN* 5.9 0.5 + - - -
349F THR* 3.4 44.9 - - + +
352F GLU* 5.0 6.1 - - + +
353F TRP* 4.2 20.4 - - + +
356F ARG* 5.6 1.6 - - - +
442F ARG* 5.5 2.7 - - - +
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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