Contacts of the helix formed by residues 458 - 466 (chain B) in PDB entry 1F1H
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 458 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320B LYS* 5.2 0.6 - - - -
456B THR 3.3 1.0 + - - +
457B PRO* 1.3 71.4 - - - +
459B PRO* 1.3 72.4 - - + +
460B VAL* 2.9 51.5 - - + +
461B GLU* 2.7 53.5 + - + +
462B PHE* 3.5 6.7 - - - -
147H SER* 4.9 0.6 + - - -
320H LYS* 5.0 2.2 - - - +
453H VAL* 4.0 21.8 + - + +
456H THR* 2.8 39.0 - - - +
457H PRO 3.7 9.8 + - - -
458H HIS* 3.4 29.6 + - + +
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Residues in contact with PRO 459 (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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147B SER* 4.2 3.4 - - - +
457B PRO 4.0 5.4 - - - +
458B HIS* 1.3 90.8 - - + +
460B VAL* 1.3 56.7 + - + +
462B PHE* 3.0 34.2 + - + +
463B GLU* 3.5 4.2 + - - +
140H PHE* 4.4 5.9 - - - +
141H GLY 4.2 4.7 - - - +
147H SER* 3.7 13.5 - - - -
148H HIS* 3.6 40.6 - - - +
149H VAL* 4.2 10.9 - - + +
459H PRO* 3.7 31.2 - - + -
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Residues in contact with VAL 460 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458B HIS* 2.9 29.6 - - + +
459B PRO* 1.3 73.6 - - + +
461B GLU* 1.3 58.2 + - - +
462B PHE 3.1 0.4 - - - -
463B GLU* 3.2 8.2 + - - +
464B LEU* 3.0 46.0 + - + +
142H ALA* 3.9 20.6 - - + -
147H SER* 5.4 0.2 - - - -
452H ARG* 3.9 36.3 - - + +
453H VAL* 4.1 7.4 - - + -
456H THR* 3.7 21.8 - - + +
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Residues in contact with GLU 461 (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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458B HIS* 2.7 43.5 + - + +
460B VAL* 1.3 73.5 - - - +
462B PHE* 1.3 55.2 + - + +
464B LEU* 4.3 0.4 - - - -
465B TYR* 2.7 51.1 + - + +
256H MET* 3.9 5.4 - - + +
316H THR* 2.6 29.2 + - - +
317H ASN* 2.9 35.9 + - + +
320H LYS* 2.7 31.6 + - - +
453H VAL* 4.0 9.3 - - + +
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Residues in contact with PHE 462 (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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457B PRO* 4.0 15.3 - - + -
458B HIS 3.5 18.2 - - - -
459B PRO 3.0 11.3 + - - +
461B GLU* 1.3 78.0 - - + +
463B GLU* 1.3 65.1 + - - +
464B LEU 3.2 0.4 - - - -
466B TYR* 3.0 34.4 + + - +
135H PHE* 5.9 0.2 - + - -
138H ILE* 4.0 19.5 - - + -
140H PHE* 3.6 26.2 - - + -
149H VAL* 3.7 39.7 - - + -
151H ILE* 4.3 3.1 - - + -
256H MET* 3.4 35.0 - - + -
259H PRO* 3.3 32.3 - - + -
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Residues in contact with GLU 463 (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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459B PRO 3.5 2.2 + - - +
460B VAL* 3.2 15.6 + - - +
462B PHE* 1.3 79.8 - - - +
464B LEU* 1.3 61.6 + - + +
466B TYR 5.0 0.2 + - - -
140H PHE* 3.4 21.7 - - + -
141H GLY* 4.2 7.3 - - - -
142H ALA* 4.0 27.5 + - - +
452H ARG* 2.7 44.7 + - - +
160I SER* 4.6 5.0 + - - -
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Residues in contact with LEU 464 (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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460B VAL* 3.0 24.7 + - + +
463B GLU* 1.3 81.0 - - + +
465B TYR* 1.3 88.3 + - + +
466B TYR 4.0 0.2 - - - -
467B SER 5.6 0.2 - - - -
468B VAL* 5.2 2.1 - - - +
449H GLU* 3.6 45.7 - - + +
452H ARG* 4.0 31.9 - - + +
453H VAL* 3.8 17.7 - - + -
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Residues in contact with TYR 465 (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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461B GLU* 2.7 38.5 + - + +
464B LEU* 1.3 101.1 - - + +
466B TYR* 1.3 66.8 + - - +
467B SER 3.2 3.1 - - - -
468B VAL* 3.0 32.3 + - + +
256H MET* 3.5 18.0 - - + +
257H PRO* 5.5 1.1 - - + -
315H THR* 3.5 44.0 - - + -
316H THR* 3.4 39.7 + - - +
317H ASN* 4.1 6.7 - - + -
414H LEU* 4.5 2.1 - - - +
446H ARG* 4.8 3.1 - - - -
449H GLU* 3.6 38.7 + - - +
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Residues in contact with TYR 466 (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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461B GLU 3.9 0.8 + - - -
462B PHE* 3.0 29.4 + + - +
463B GLU 5.0 0.2 + - - -
464B LEU 4.0 0.2 - - - -
465B TYR* 1.3 77.3 - - - +
467B SER* 1.3 57.1 + - - +
468B VAL 3.3 2.8 + - - +
135H PHE* 3.8 10.3 - + - -
138H ILE* 3.5 39.3 - - + +
140H PHE* 4.3 7.0 - + + -
243H HIS* 5.0 0.2 + - - -
252H THR* 2.7 44.0 + - - +
253H ALA 4.3 0.2 - - - -
254H THR* 2.9 51.7 + - + -
255H PHE 4.3 1.0 + - - -
256H MET* 3.7 17.2 - - - +
169I LYS 3.7 7.9 - - - -
170I GLY 3.9 11.9 - - - +
171I HIS* 3.4 32.1 - + - -
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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