Contacts of the helix formed by residues 438 - 450 (chain F) in PDB entry 3IFS
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 PHE 438 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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427F LYS* 4.0 36.1 - - + -
430F PHE* 4.0 23.3 - + + -
431F ALA* 3.5 22.2 - - + -
435F LYS* 3.2 40.3 + - + +
436F PRO 3.5 15.0 - - - -
437F GLY* 1.3 79.9 - - - +
439F GLU* 1.3 62.5 + - - +
440F GLU* 3.4 2.9 - - - -
441F LEU* 3.3 11.6 + - + +
442F LYS* 2.9 22.8 + - - +
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Residues in contact with GLU 439 (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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248C GLU* 3.1 37.5 + - + +
434F GLY* 5.9 0.2 - - - -
435F LYS 4.6 0.6 + - - -
437F GLY 3.5 0.2 - - - -
438F PHE* 1.3 76.6 - - - +
440F GLU* 1.3 64.9 + - - +
442F LYS* 3.1 29.0 + - - +
443F ALA* 2.9 33.1 + - + +
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Residues in contact with GLU 440 (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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4C HIS* 3.3 14.1 + - - -
240C ASP* 3.2 4.8 - - - +
248C GLU* 4.7 0.4 + - - -
451C LI 1.8 48.0 - - - +
437F GLY 5.2 1.5 + - - +
438F PHE 3.4 0.6 - - - -
439F GLU* 1.3 78.4 - - - +
441F LEU* 1.3 62.0 + - - +
443F ALA* 3.3 6.5 + - - +
444F GLU* 3.1 24.8 + - - +
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Residues in contact with LEU 441 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427F LYS* 3.7 35.0 - - + +
428F ASN* 3.9 13.2 - - - +
431F ALA* 3.9 14.6 - - + -
438F PHE* 3.3 15.7 + - + +
439F GLU 3.3 0.2 - - - -
440F GLU* 1.3 78.8 - - - +
442F LYS* 1.3 57.6 + - - +
444F GLU* 3.1 30.5 + - - +
445F LEU* 2.8 47.1 + - + +
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Residues in contact with LYS 442 (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 ALA* 3.3 33.8 - - - +
432F LEU* 4.3 13.2 - - - -
434F GLY* 4.3 14.6 - - - -
438F PHE 2.9 14.5 + - - +
439F GLU* 3.4 32.3 + - - +
441F LEU* 1.3 76.7 - - - +
443F ALA* 1.3 57.5 + - - +
445F LEU* 3.3 4.5 + - - +
446F GLU* 2.5 72.9 + - + +
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Residues in contact with ALA 443 (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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439F GLU* 2.9 25.6 + - + +
440F GLU* 3.7 5.6 - - - +
442F LYS* 1.3 77.5 - - - +
444F GLU* 1.3 63.4 + - - +
446F GLU* 3.5 9.2 + - - +
447F GLU* 3.2 22.7 + - - +
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Residues in contact with GLU 444 (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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440F GLU* 3.1 15.0 + - - +
441F LEU* 3.1 30.2 + - + +
443F ALA* 1.3 79.0 - - - +
445F LEU* 1.3 67.2 + - + +
447F GLU* 3.5 7.0 + - - +
448F ARG* 3.5 33.5 + - - +
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Residues in contact with LEU 445 (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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372E LEU* 3.9 22.0 - - + +
428F ASN* 3.6 59.2 - - + +
431F ALA* 4.1 3.8 - - + -
432F LEU* 3.9 17.9 - - + -
441F LEU* 2.8 41.8 + - + +
442F LYS 3.9 2.7 - - - +
444F GLU* 1.3 76.5 - - - +
446F GLU* 1.3 65.5 + - - +
448F ARG* 3.0 31.9 + - - +
449F LEU* 3.1 17.3 + - - +
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Residues in contact with GLU 446 (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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365E LYS* 5.2 6.9 + - - +
432F LEU* 3.8 18.9 - - + +
442F LYS* 2.5 64.2 + - - +
443F ALA* 4.0 7.2 - - - +
445F LEU* 1.3 75.8 - - - +
447F GLU* 1.3 61.6 + - - +
449F LEU* 3.1 21.0 + - + +
450F LYS* 3.3 14.8 + - - +
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Residues in contact with GLU 447 (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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443F ALA 3.2 13.6 + - - +
444F GLU* 3.5 12.1 - - - +
445F LEU 3.2 0.4 - - - -
446F GLU* 1.3 77.0 - - - +
448F ARG* 1.3 64.8 + - + +
449F LEU 3.4 0.5 + - - -
450F LYS* 3.1 53.1 + - - +
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Residues in contact with ARG 448 (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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11E LYS* 4.2 14.2 - - - +
372E LEU* 3.8 37.2 + - + +
375E SER* 4.6 6.7 - - - -
376E ASP* 2.8 42.4 + - - -
444F GLU* 3.5 25.7 + - - +
445F LEU* 3.0 28.1 + - - +
447F GLU* 1.3 79.8 - - + +
449F LEU* 1.3 62.0 + - - +
450F LYS 3.6 1.6 + - - -
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Residues in contact with LEU 449 (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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11E LYS* 3.5 21.4 + - - +
368E GLU* 3.7 48.5 - - + +
371E LEU* 5.2 5.8 - - + -
372E LEU* 3.9 25.6 - - + -
432F LEU* 4.1 20.4 - - + -
445F LEU 3.1 13.9 + - - +
446F GLU* 3.1 14.1 + - + +
448F ARG* 1.3 78.3 - - - +
450F LYS* 1.3 70.0 + - - +
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Residues in contact with LYS 450 (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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11E LYS* 4.1 11.4 + - - -
446F GLU 3.3 10.1 + - - +
447F GLU* 3.1 46.3 + - - +
448F ARG 3.4 3.6 - - - -
449F LEU* 1.3 88.8 - - - +
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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