Contacts of the helix formed by residues 458 - 466 (chain K) in PDB entry 1FPY
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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147E SER* 4.7 0.6 + - - -
320E LYS* 4.4 3.1 - - - +
453E VAL* 4.2 20.1 + - + +
456E THR* 2.8 49.5 - - - +
457E PRO 3.1 14.5 + - - -
458E HIS* 3.1 30.1 + - + +
320K LYS* 5.3 1.0 + - - -
456K THR 3.4 0.8 + - - -
457K PRO* 1.3 73.4 - - - +
459K PRO* 1.3 79.8 - - + +
460K VAL* 2.9 40.5 - - + +
461K GLU* 2.8 40.8 + - + +
462K PHE* 3.4 6.6 - - - -
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Residues in contact with PRO 459 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140E PHE* 4.5 4.0 - - - +
141E GLY 4.4 4.3 - - - +
147E SER* 3.8 15.7 - - - +
148E HIS* 3.5 39.0 - - - +
149E VAL* 4.2 3.5 - - + +
459E PRO* 3.5 36.3 - - + -
147K SER* 4.1 7.4 - - - +
457K PRO 4.1 3.8 - - - +
458K HIS* 1.3 91.8 - - + -
460K VAL* 1.3 53.1 + - - +
462K PHE* 2.7 43.2 + - + +
463K GLU* 3.5 3.4 + - - +
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Residues in contact with VAL 460 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142E ALA* 4.1 13.9 - - + -
452E ARG* 4.1 33.2 - - + +
453E VAL* 4.0 12.3 - - + +
456E THR* 3.7 22.2 - - + +
458K HIS* 2.9 29.5 - - + +
459K PRO* 1.3 75.0 - - + +
461K GLU* 1.3 55.9 + - - +
462K PHE 3.1 0.2 - - - -
463K GLU* 3.1 9.7 + - + +
464K LEU* 2.8 49.7 + - + +
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Residues in contact with GLU 461 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256E MET* 3.9 3.9 - - + +
316E THR* 2.7 27.0 + - - +
317E ASN* 2.8 44.1 + - + +
320E LYS* 3.0 33.3 + - - +
453E VAL* 4.1 6.9 - - + +
457K PRO* 3.6 0.5 - - - +
458K HIS* 2.8 36.6 + - + +
460K VAL* 1.3 76.9 - - - +
462K PHE* 1.3 53.3 + - + +
465K TYR* 2.5 54.0 + - + +
466K TYR 3.8 0.2 + - - -
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Residues in contact with PHE 462 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135E PHE* 6.3 0.2 - + - -
138E ILE* 4.4 5.6 - - + -
140E PHE* 3.6 27.5 - - + -
149E VAL* 3.5 39.5 - - + -
151E ILE* 4.4 7.2 - - + -
256E MET* 3.4 31.9 - - + -
259E PRO* 3.2 37.2 - - + -
457K PRO* 4.0 14.1 - - + -
458K HIS 3.4 14.1 - - - -
459K PRO 2.7 16.4 + - - +
461K GLU* 1.3 75.6 - - + +
463K GLU* 1.3 68.7 + - - +
466K TYR* 2.9 42.4 + + + +
467K SER 4.7 0.3 + - - -
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Residues in contact with GLU 463 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140E PHE* 3.4 26.8 - - + -
141E GLY* 4.6 4.0 - - - -
142E ALA* 4.0 24.6 + - - +
452E ARG* 2.6 42.0 + - - +
459K PRO 3.5 1.6 + - - +
460K VAL* 3.3 15.5 - - - +
462K PHE* 1.3 83.5 - - - +
464K LEU* 1.3 60.2 + - + +
466K TYR 5.0 0.2 + - - -
467K SER 5.9 0.2 + - - -
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Residues in contact with LEU 464 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449E GLU* 3.6 44.8 - - + +
452E ARG* 3.6 32.8 - - + +
453E VAL* 3.8 11.9 - - + -
460K VAL* 2.8 31.2 + - + +
463K GLU* 1.3 84.0 - - + +
465K TYR* 1.3 84.9 + - + +
467K SER 5.5 0.2 + - - -
468K VAL* 5.2 1.9 - - - +
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Residues in contact with TYR 465 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256E MET* 3.7 18.8 - - + +
257E PRO* 5.6 0.7 - - + -
314E PRO 4.1 1.7 + - - -
315E THR* 3.4 43.2 - - + -
316E THR* 3.3 39.1 + - - +
317E ASN* 4.1 4.9 - - + -
414E LEU* 4.5 1.6 - - - +
446E ARG* 4.6 3.6 - - - -
449E GLU* 3.4 41.4 + - - +
461K GLU* 2.5 41.1 + - + +
464K LEU* 1.3 99.6 - - + +
466K TYR* 1.3 66.9 + - - +
467K SER 3.2 2.5 - - - -
468K VAL* 2.9 35.8 + - + +
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Residues in contact with TYR 466 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169D LYS 4.6 1.8 - - - -
170D GLY 4.5 6.7 - - - -
171D HIS* 3.4 29.8 - + - -
135E PHE* 3.8 13.2 - + - -
138E ILE* 3.6 42.4 - - + +
140E PHE* 4.5 7.9 - + + -
243E HIS* 4.9 0.5 + - - -
252E THR* 2.6 38.5 + - - +
253E ALA 4.0 0.9 - - - -
254E THR* 2.8 55.2 + - + -
255E PHE 4.2 1.9 + - - -
256E MET* 3.8 15.6 - - - -
461K GLU 3.8 2.0 + - - -
462K PHE* 2.9 30.4 + + + +
465K TYR* 1.3 77.7 - - - +
467K SER* 1.3 62.8 + - - +
468K VAL 3.1 4.3 + - - +
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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