Contacts of the helix formed by residues 450 - 455 (chain B) in PDB entry 5FPP
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 GLU 450 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202B GLU* 3.4 9.1 - - - +
228B GLN* 3.1 41.3 + - - +
229B SER* 4.0 5.8 + - - -
331B VAL* 3.8 15.1 - - + +
428B TYR* 4.3 9.4 + - + +
430B PHE* 3.6 41.7 - - + -
448B GLY* 3.2 22.2 + - - -
449B TYR* 1.3 74.1 + - - +
451B ILE* 1.3 70.4 + - - +
452B GLU 3.4 1.1 - - - -
453B PHE* 3.0 16.5 + - - +
454B ILE* 3.1 19.4 + - + +
480B TRP* 6.2 0.2 - - + -
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Residues in contact with ILE 451 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B TRP* 4.3 9.6 - - + -
117B TRP* 4.3 3.4 - - + -
132B VAL* 3.5 24.0 - - + +
133B TYR* 3.9 24.5 - - + +
202B GLU* 3.7 36.1 - - + +
228B GLN* 4.1 7.2 - - - +
448B GLY* 3.5 19.3 - - - +
449B TYR 3.4 1.2 - - - -
450B GLU* 1.3 92.8 - - - +
452B GLU* 1.3 59.0 + - - +
453B PHE 3.1 0.3 + - - -
454B ILE* 3.2 6.0 + - - +
455B PHE* 2.9 46.9 + - + -
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Residues in contact with GLU 452 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B MET* 4.4 9.7 - - - +
132B VAL* 4.1 19.5 - - + +
434B ALA* 3.8 12.1 - - - +
436B THR* 4.2 2.9 + - - -
448B GLY 4.8 1.5 + - - +
449B TYR* 3.5 37.4 - - - +
451B ILE* 1.3 79.0 - - - +
453B PHE* 1.3 74.7 + - + +
455B PHE 4.0 0.3 - - - -
456B GLY 3.3 4.0 + - - -
457B LEU* 2.9 42.6 + - + +
458B PRO* 3.3 3.5 - - - +
465B TYR* 2.4 38.4 + - + +
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Residues in contact with PHE 453 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430B PHE* 3.6 20.2 - + + -
432B HIS* 3.5 24.9 - + - -
434B ALA* 3.9 22.0 - - + -
449B TYR 3.6 18.6 - - - -
450B GLU 3.0 7.0 + - - +
452B GLU* 1.3 83.4 - - + +
454B ILE* 1.3 66.9 + - - +
456B GLY* 3.0 14.6 + - - -
458B PRO* 3.6 26.2 - - + -
465B TYR* 4.0 6.5 - + - -
469B GLU* 3.8 33.2 - - + -
472B PHE* 3.9 13.7 - + - -
473B ALA* 3.7 18.1 - - + +
476B LEU* 3.7 19.3 - - + -
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Residues in contact with ILE 454 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138B LEU* 3.9 9.5 - - + +
200B PHE* 4.4 15.0 - - + -
228B GLN* 4.5 6.7 - - - +
430B PHE* 5.4 2.2 - - + -
450B GLU* 3.1 26.7 + - + +
451B ILE* 3.7 5.8 - - - +
453B PHE* 1.3 74.6 - - - +
455B PHE* 1.3 65.6 + - + +
476B LEU* 3.7 26.7 - - + +
477B MET* 3.2 20.1 - - - +
480B TRP* 3.5 72.9 - - + +
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Residues in contact with PHE 455 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B TRP* 3.5 45.8 - + - -
132B VAL 3.4 15.9 - - - +
133B TYR* 3.3 26.7 - - + -
134B ASP 3.4 21.0 - - - +
135B GLY* 4.4 0.4 - - - -
137B PHE* 3.2 25.8 - - - +
138B LEU* 4.1 15.3 + - + +
146B LEU* 4.3 17.5 - - + -
200B PHE* 3.7 20.6 - + - -
451B ILE* 2.9 33.7 + - + +
454B ILE* 1.3 80.3 - - + +
456B GLY* 1.3 58.6 + - - +
457B LEU* 3.4 13.0 - - + -
477B MET* 4.6 1.6 - - - -
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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