Contacts of the helix formed by residues 484 - 491 (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 GLY 484 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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401E GLU* 4.8 17.1 + - - -
404E LEU* 5.6 4.0 - - - -
482F GLN 3.2 1.0 - - - -
483F GLN* 1.3 76.2 - - - +
485F ARG* 1.3 58.1 + - - +
486F PHE 3.4 2.7 - - - -
487F ALA* 3.4 13.5 + - - +
488F LYS* 3.0 35.0 + - - +
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Residues in contact with ARG 485 (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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431F MET* 2.7 40.3 + - + +
432F ARG* 3.0 23.0 + - - +
433F MET* 3.6 2.6 - - - +
437F GLU* 2.6 44.6 + - - +
475F CYS* 4.2 14.8 - - + -
479F TYR* 3.8 34.4 - - + -
482F GLN* 3.2 51.4 + - + +
483F GLN 3.4 0.8 - - - -
484F GLY* 1.3 74.7 - - - +
486F PHE* 1.3 67.4 + - - +
488F LYS* 3.2 11.4 + - - +
489F LEU* 3.0 23.5 + - + +
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Residues in contact with PHE 486 (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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404E LEU* 6.1 0.2 - - + -
418E PHE* 4.5 13.2 - + - -
419E PRO* 4.1 25.4 - - + -
468F TYR* 3.6 29.6 - - - -
471F LEU* 3.8 25.1 - - + -
472F GLU* 3.3 49.4 - - + +
475F CYS* 4.1 19.9 - - + +
476F LYS* 6.5 0.4 - - + -
482F GLN 5.0 0.2 + - - -
483F GLN 5.0 3.5 + - - +
484F GLY 3.4 0.4 - - - -
485F ARG* 1.3 77.6 - - - +
487F ALA* 1.3 62.8 + - - +
489F LEU* 3.2 6.9 + - - +
490F LEU* 3.2 47.7 + - + +
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Residues in contact with ALA 487 (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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400E VAL* 3.9 18.4 - - + -
404E LEU* 5.9 3.8 - - + -
418E PHE* 3.8 29.2 - - + -
422E LEU* 4.3 10.3 - - + -
484F GLY* 3.4 14.1 + - - +
485F ARG 3.3 0.4 - - - -
486F PHE* 1.3 76.7 - - - +
488F LYS* 1.3 66.5 - - - +
489F LEU 3.1 0.2 + - - -
490F LEU* 3.2 2.8 + - - +
491F LEU* 2.9 30.9 + - + +
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Residues in contact with LYS 488 (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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397E GLN* 4.9 15.9 + - - -
431F MET* 3.8 27.2 - - + +
482F GLN* 5.8 4.5 + - - +
484F GLY 3.0 18.3 + - - +
485F ARG* 3.3 14.6 - - - +
487F ALA* 1.3 76.5 - - - +
489F LEU* 1.3 63.4 + - - +
491F LEU* 3.6 15.2 + - + +
492F ARG* 3.8 18.0 + - - +
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Residues in contact with LEU 489 (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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431F MET* 3.4 28.7 - - + -
433F MET* 4.0 26.0 - - + -
437F GLU* 3.9 21.5 - - + +
441F LEU* 3.9 25.5 - - + +
471F LEU* 4.0 19.5 - - + -
475F CYS* 3.6 31.2 - - - -
485F ARG* 3.0 16.4 + - + +
486F PHE* 3.5 7.6 - - - +
487F ALA 3.1 0.2 - - - -
488F LYS* 1.3 75.7 - - - +
490F LEU* 1.3 65.3 + - - +
492F ARG* 3.1 23.2 + - - +
493F LEU 4.2 0.9 + - - -
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Residues in contact with LEU 490 (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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419E PRO* 3.8 26.0 - - + +
422E LEU* 4.2 20.2 - - + -
423E MET* 3.9 17.7 - - + +
441F LEU* 4.2 8.3 - - + -
444F ILE* 3.9 27.6 - - + -
468F TYR* 4.8 4.9 - - + -
471F LEU* 4.5 1.6 - - + -
486F PHE* 3.2 45.9 + - + +
487F ALA 3.2 6.6 + - - +
489F LEU* 1.3 79.8 - - - +
491F LEU* 1.3 56.5 + - - +
493F LEU* 3.0 37.6 + - + +
494F PRO* 3.4 3.8 - - - +
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Residues in contact with LEU 491 (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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376E ILE* 4.8 2.7 - - + -
396E GLN* 3.7 31.9 - - - +
400E VAL* 3.9 22.0 - - + -
422E LEU* 4.4 19.1 - - + -
425E LEU* 4.1 26.5 - - + -
487F ALA* 2.9 26.4 + - + +
488F LYS* 4.0 10.8 - - + +
489F LEU 3.2 0.6 - - - -
490F LEU* 1.3 72.2 - - - +
492F ARG* 1.3 80.6 + - - +
493F LEU 3.3 0.4 - - - -
494F PRO* 3.5 15.3 - - + +
495F ALA* 4.5 3.8 + - - +
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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