Contacts of the helix formed by residues 458 - 466 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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320D LYS* 5.3 0.8 + - - -
456D THR 3.4 1.0 + - - -
457D PRO* 1.3 72.8 - - - +
459D PRO* 1.3 80.7 - - + +
460D VAL* 2.9 40.2 - - + +
461D GLU* 2.8 40.1 + - + +
462D PHE* 3.4 6.8 - - - -
147J SER* 4.7 0.4 + - - -
320J LYS* 4.5 2.9 - - - +
453J VAL* 4.2 19.0 + - + +
456J THR* 2.8 51.5 - - + +
457J PRO 3.1 17.2 + - - -
458J HIS* 3.2 26.8 + - + +
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Residues in contact with PRO 459 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147D SER* 4.1 6.7 - - - +
457D PRO 4.0 3.8 - - - +
458D HIS* 1.3 92.0 - - + +
460D VAL* 1.3 52.3 + - - +
462D PHE* 2.7 42.4 + - + +
463D GLU* 3.5 3.2 + - - +
140J PHE* 4.5 3.6 - - - +
141J GLY 4.3 4.3 - - - +
147J SER* 3.7 16.4 - - - +
148J HIS* 3.5 41.7 - - - +
149J VAL* 4.2 3.1 - - + +
459J PRO* 3.5 35.7 - - + -
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Residues in contact with VAL 460 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458D HIS* 2.9 30.2 - - + +
459D PRO* 1.3 76.4 - - + +
461D GLU* 1.3 56.3 + - - +
462D PHE 3.1 0.2 - - - -
463D GLU* 3.1 10.1 + - + +
464D LEU* 2.8 48.5 + - + +
142J ALA* 4.0 13.9 - - + -
452J ARG* 4.0 33.0 - - + +
453J VAL* 4.1 11.9 - - + +
456J THR* 3.7 22.0 - - + +
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Residues in contact with GLU 461 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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457D PRO* 3.6 4.3 - - - +
458D HIS* 2.8 40.3 + - + +
460D VAL* 1.3 77.9 - - - +
462D PHE* 1.3 54.1 + - + +
465D TYR* 2.5 53.6 + - + +
256J MET* 3.9 5.2 - - + +
316J THR* 2.7 28.2 + - - +
317J ASN* 2.8 45.1 + - + +
320J LYS* 3.0 25.1 + - - +
453J VAL* 4.0 6.9 - - + +
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Residues in contact with PHE 462 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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457D PRO* 4.0 14.6 - - + -
458D HIS 3.4 14.6 - - - -
459D PRO 2.7 15.4 + - - +
461D GLU* 1.3 75.5 - - + +
463D GLU* 1.3 68.5 + - - +
466D TYR* 2.9 41.3 + + + +
467D SER 4.7 0.2 + - - -
135J PHE* 6.4 0.2 - + - -
138J ILE* 4.4 6.3 - - + -
140J PHE* 3.5 28.3 - - + -
149J VAL* 3.5 39.5 - - + -
151J ILE* 4.5 7.4 - - + -
256J MET* 3.4 31.4 - - + -
259J PRO* 3.3 34.8 - - + -
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Residues in contact with GLU 463 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459D PRO 3.5 2.0 + - - -
460D VAL* 3.3 15.1 - - - +
462D PHE* 1.3 82.3 - - - +
464D LEU* 1.3 60.9 + - + +
466D TYR 5.0 0.3 + - - -
140J PHE* 3.3 24.9 - - + -
141J GLY* 4.6 3.3 - - - -
142J ALA* 4.0 25.1 + - - +
452J ARG* 2.6 41.4 + - - +
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Residues in contact with LEU 464 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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460D VAL* 2.8 32.2 + - + +
463D GLU* 1.3 81.8 - - + +
465D TYR* 1.3 84.4 + - + +
467D SER 5.5 0.4 + - - -
468D VAL* 5.2 2.1 - - - +
449J GLU* 3.6 44.3 - - + +
452J ARG* 3.5 34.3 - - + +
453J VAL* 3.8 10.5 - - + -
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Residues in contact with TYR 465 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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461D GLU* 2.5 41.6 + - + +
464D LEU* 1.3 100.4 - - + +
466D TYR* 1.3 66.6 + - - +
467D SER 3.2 3.4 - - - -
468D VAL* 2.9 35.2 + - + +
256J MET* 3.8 17.6 - - + +
257J PRO* 5.7 0.2 - - + -
314J PRO 4.2 1.1 + - - -
315J THR* 3.4 43.6 - - + -
316J THR* 3.3 39.0 + - - +
317J ASN* 4.2 5.2 - - + -
414J LEU* 4.5 1.6 - - - +
446J ARG* 4.6 2.7 - - - -
449J GLU* 3.4 43.2 + - - +
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Residues in contact with TYR 466 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461D GLU 3.8 2.0 + - - -
462D PHE* 2.9 30.8 + + - +
463D GLU 5.0 0.2 + - - -
464D LEU 3.9 0.2 - - - -
465D TYR* 1.3 77.1 - - - +
467D SER* 1.3 62.4 + - - +
468D VAL 3.1 4.0 + - - +
135J PHE* 3.8 11.2 - + - -
138J ILE* 3.5 42.4 - - + +
140J PHE* 4.4 7.6 - + + -
243J HIS* 4.9 0.3 + - - -
252J THR* 2.6 38.7 + - - +
253J ALA 4.0 1.6 + - - -
254J THR* 2.9 55.0 + - + -
255J PHE 4.2 2.1 + - - -
256J MET* 3.9 15.8 - - - -
169K LYS 4.5 2.2 - - - -
170K GLY 4.4 7.6 - - - -
171K HIS* 3.2 31.9 - + - -
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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