Contacts of the helix formed by residues 466 - 474 (chain X) in PDB entry 1FM6
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 HIS 466 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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286X GLN* 2.9 17.0 + - + +
287X PHE* 4.1 26.9 - + + -
290X VAL* 3.5 29.1 - - + +
465X LEU* 1.3 72.0 - - - +
467X PRO* 1.3 69.3 - - + +
468X LEU* 2.9 41.9 + - + +
469X LEU* 2.8 35.5 + - + +
470X GLN* 2.8 15.5 + - - +
689Y ILE* 5.1 4.3 - - + -
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Residues in contact with PRO 467 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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465X LEU 3.3 3.8 - - - +
466X HIS* 1.3 100.4 - - + +
468X LEU* 1.3 59.7 + - - +
470X GLN* 3.4 18.8 + - + +
471X GLU* 3.2 24.6 + - - +
689Y ILE* 4.4 13.2 - - + +
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Residues in contact with LEU 468 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290X VAL* 4.0 37.5 - - + +
293X VAL* 4.1 15.9 - - + -
294X GLN* 5.1 3.6 - - - +
466X HIS* 2.9 20.7 + - + +
467X PRO* 1.3 72.9 - - - +
469X LEU* 1.3 67.5 + - + +
470X GLN 3.0 1.6 - - - -
471X GLU* 3.2 17.9 + - - +
472X ILE* 3.2 20.9 + - + +
689Y ILE* 3.9 36.5 - - + +
690Y LEU* 3.6 30.3 - - + +
693Y LEU* 4.8 5.4 - - + -
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Residues in contact with LEU 469 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286X GLN* 3.6 47.8 - - + +
289X SER* 4.1 15.0 - - - -
290X VAL* 4.4 10.3 - - + +
293X VAL* 5.0 2.2 - - + -
323X HIS* 4.4 8.7 - - + +
465X LEU* 4.5 5.2 - - + -
466X HIS* 2.8 20.3 + - + +
468X LEU* 1.3 80.0 - - + +
470X GLN* 1.3 61.9 + - - +
472X ILE* 3.9 14.9 - - + +
473X TYR* 3.0 41.2 + - + -
504X BRL 3.9 28.5 - - - +
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Residues in contact with GLN 470 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464X SER* 5.4 1.8 - - - +
465X LEU* 2.8 40.1 + - + +
466X HIS 2.8 9.3 + - - +
467X PRO* 3.4 22.1 - - - +
468X LEU 3.0 0.2 - - - -
469X LEU* 1.3 75.1 - - - +
471X GLU* 1.3 65.0 + - - +
473X TYR* 3.3 3.9 + - - +
474X LYS* 3.0 25.7 + - - +
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Residues in contact with GLU 471 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319X LYS* 3.1 17.7 + - - -
467X PRO 3.2 9.4 + - - +
468X LEU* 3.2 11.4 + - + +
470X GLN* 1.3 81.8 - - - +
472X ILE* 1.3 60.0 + - + +
474X LYS* 3.6 11.4 + - - +
686Y ARG* 4.3 6.4 + - - +
687Y HIS* 3.0 47.0 - - - +
688Y LYS* 3.5 11.5 + - + +
689Y ILE* 2.6 46.0 + - - +
690Y LEU* 3.4 10.7 + - - +
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Residues in contact with ILE 472 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293X VAL* 4.0 24.0 - - + -
318X LEU 6.0 0.2 - - - +
319X LYS* 2.8 51.2 + - - +
322X VAL* 4.5 9.4 - - + -
323X HIS* 3.9 22.0 - - + +
468X LEU* 3.2 34.6 + - + +
469X LEU* 4.0 12.6 - - + +
471X GLU* 1.3 75.9 - - + +
473X TYR* 1.3 60.6 + - - +
476X LEU* 3.5 13.5 - - + +
687Y HIS* 4.8 0.9 - - - -
690Y LEU* 4.2 24.9 - - + -
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Residues in contact with TYR 473 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323X HIS* 3.2 35.7 + + - -
446X VAL* 5.4 3.1 - - + -
449X HIS* 3.3 15.8 - + - -
450X VAL* 3.8 25.9 - - + +
453X LEU* 3.5 20.2 - - + -
465X LEU* 3.7 22.4 - - + -
469X LEU* 3.0 32.0 + - + +
470X GLN* 4.1 3.6 - - - +
472X ILE* 1.3 75.3 - - - +
474X LYS* 1.3 67.6 + - - +
475X ASP 2.9 2.1 + - - -
476X LEU* 2.9 31.7 + - + +
504X BRL 2.8 30.6 + - - -
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Residues in contact with LYS 474 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319X LYS* 2.7 25.6 + - - -
470X GLN 3.0 18.3 + - - +
471X GLU* 3.6 11.4 - - - +
472X ILE 3.3 1.2 - - - -
473X TYR* 1.3 73.5 - - - +
475X ASP* 1.3 79.9 + - - +
686Y ARG* 3.2 43.8 + - - +
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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