Contacts of the helix formed by residues 312 - 320 (chain F) in PDB entry 5JLH
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 312 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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310F GLY 3.7 3.8 + - - -
311F ALA* 1.3 72.8 - - - +
313F GLU* 1.3 56.0 + - - -
314F GLN* 3.0 9.5 + - - +
315F LEU* 3.1 4.6 + - - +
316F LYS* 2.6 38.2 + - - +
342F ARG* 5.1 11.4 - - - -
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Residues in contact with GLU 313 (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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312F GLY* 1.3 70.8 - - - -
314F GLN* 1.3 66.1 + - + +
315F LEU 3.2 0.2 - - - -
316F LYS* 4.1 16.4 - - - +
317F ALA* 2.9 35.7 + - + +
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Residues in contact with GLN 314 (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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312F GLY* 3.0 5.6 - - - -
313F GLU* 1.3 86.3 - - + +
315F LEU* 1.3 60.6 + - + +
317F ALA* 4.7 1.0 - - - +
318F ASP* 3.4 20.6 + - - +
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Residues in contact with LEU 315 (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 LEU* 4.5 0.2 - - + -
311F ALA* 3.9 19.1 - - + -
312F GLY 3.1 7.5 + - - +
314F GLN* 1.3 78.4 - - + +
316F LYS* 1.3 67.8 + - - +
317F ALA 3.2 1.8 - - - -
318F ASP* 3.1 7.3 + - - +
319F LEU* 2.9 70.9 + - + +
321F LEU* 4.7 0.4 - - + -
345F PHE* 4.1 15.3 - - + -
349F LEU* 4.7 11.2 - - + -
359F HIS* 5.4 11.4 - - + +
362F ILE* 5.7 3.1 - - + -
363F ILE* 5.0 12.6 - - + -
366F LEU* 3.9 26.2 - - + -
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Residues in contact with LYS 316 (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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308F LEU 5.1 8.1 - - - +
311F ALA* 4.3 13.4 - - + +
312F GLY 2.6 24.6 + - - +
313F GLU* 4.1 12.1 - - - +
315F LEU* 1.3 74.4 - - - +
317F ALA* 1.3 52.8 + - - +
319F LEU 4.4 0.4 - - - +
320F LEU* 2.5 37.6 + - - +
321F LEU* 3.3 50.0 + - + +
322F GLU* 5.2 2.9 - - - -
323F PRO* 5.1 11.9 - - - +
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Residues in contact with ALA 317 (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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313F GLU* 2.9 24.9 + - + +
314F GLN 4.7 2.2 - - - +
316F LYS* 1.3 77.9 - - - +
318F ASP* 1.3 58.4 + - - +
320F LEU* 3.0 22.2 - - - +
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Residues in contact with ASP 318 (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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314F GLN 3.4 17.6 - - - +
315F LEU* 3.1 7.8 + - - +
317F ALA* 1.3 80.1 - - - +
319F LEU* 1.4 61.9 + - + +
320F LEU* 2.9 15.9 - - - +
363F ILE* 3.3 25.8 - - + +
367F ARG* 4.0 25.6 + - - +
402F ARG* 5.3 1.6 + - - -
403F LEU* 5.2 2.6 - - - +
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Residues in contact with LEU 319 (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 LEU* 4.1 2.0 - - + -
315F LEU* 2.9 45.0 + - + +
318F ASP* 1.4 82.5 - - + +
320F LEU* 1.3 72.2 + - - +
321F LEU* 3.7 31.9 - - + -
363F ILE* 4.1 12.8 - - + +
366F LEU* 3.1 34.8 - - + +
367F ARG* 3.7 32.8 - - + +
370F SER* 3.7 13.7 + - - -
374F GLN* 4.8 1.2 + - - -
399F LYS* 4.8 0.3 - - - +
403F LEU* 4.5 10.0 - - - +
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Residues in contact with LEU 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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316F LYS 2.5 17.7 + - - -
317F ALA* 3.0 20.9 - - - +
318F ASP 2.9 28.9 - - - +
319F LEU* 1.3 75.1 - - - +
321F LEU* 1.3 62.8 + - - +
322F GLU* 3.9 0.4 + - - -
327F TYR* 4.0 0.3 + - - -
374F GLN* 3.7 5.4 + - - -
399F LYS* 2.9 58.3 + - + +
402F ARG* 3.4 38.4 - - + +
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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