Contacts of the helix formed by residues 317 - 322 (chain E) 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 ASN 317 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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256E MET* 3.6 19.8 - - + +
257E PRO* 3.1 12.4 - - + +
258E LYS* 2.5 54.3 + - - +
315E THR* 3.6 7.4 - - - +
316E THR* 1.3 80.9 + - - +
318E SER* 1.3 55.9 + - - +
320E LYS* 2.7 32.7 + - - +
321E ARG 3.5 2.9 + - - -
457K PRO* 4.2 4.2 - - - +
461K GLU* 2.8 33.2 + - + +
465K TYR* 4.1 13.5 - - + -
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Residues in contact with SER 318 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257E PRO* 3.7 7.0 - - - +
313E ASN* 3.5 25.2 - - - -
314E PRO* 3.9 0.7 - - - +
315E THR* 2.5 40.4 + - - +
317E ASN* 1.3 71.7 - - - +
319E TYR* 1.3 58.1 + - - +
321E ARG* 3.3 23.0 + - - +
322E LEU* 3.5 12.8 + - - +
362E ASP* 2.7 36.9 + - - +
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Residues in contact with TYR 319 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309E ASN* 3.8 4.1 - - + +
313E ASN* 2.9 30.8 + - + +
315E THR 3.1 27.8 - - - -
316E THR* 3.4 11.2 - - - +
317E ASN 3.0 1.0 - - - -
318E SER* 1.3 73.8 - - - +
320E LYS* 1.3 61.9 + - + +
321E ARG 3.2 1.7 + - - -
322E LEU* 3.8 37.2 + - + +
323E VAL* 4.4 5.2 - - - +
411E ALA* 3.4 27.4 - - + -
412E GLY 3.9 15.2 - - - +
413E SER* 3.1 21.5 - - - -
414E LEU* 3.4 27.5 - - + +
417E ALA* 3.0 24.8 - - - +
454K ARG* 4.9 7.9 + - - +
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Residues in contact with LYS 320 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258E LYS* 3.7 27.2 - - + +
316E THR* 3.8 11.8 + - - +
317E ASN* 2.7 18.3 + - - +
319E TYR* 1.3 74.3 - - + +
321E ARG* 1.3 60.5 + - - +
323E VAL* 3.6 18.3 - - - +
453E VAL* 4.4 12.5 - - - +
458E HIS* 5.3 1.0 + - - -
453K VAL 4.1 6.9 + - - -
454K ARG* 3.4 26.2 + - - +
455K MET* 3.4 22.3 - - - +
456K THR 3.3 25.3 + - - -
457K PRO* 4.3 1.8 - - + -
458K HIS* 4.4 4.4 - - - +
461K GLU* 3.0 37.8 + - - +
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Residues in contact with ARG 321 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257E PRO* 4.0 13.0 - - + +
258E LYS* 3.9 26.8 + - + +
265E GLY* 4.3 4.0 - - - -
266E SER 3.3 21.0 + - - -
267E GLY* 3.6 7.7 - - - -
317E ASN 3.5 1.2 + - - +
318E SER 3.3 10.7 + - - +
320E LYS* 1.3 79.3 - - - +
322E LEU* 1.3 70.8 + - - +
323E VAL* 2.8 22.2 + - - +
326E TYR* 5.1 0.5 - - - -
328E ALA* 3.2 21.5 - - + +
329E PRO* 5.2 0.2 - - - +
359E ARG* 3.3 23.6 + - - +
360E PHE* 3.1 21.2 + - - +
361E PRO 3.5 8.2 + - - -
362E ASP* 3.7 13.9 + - - +
5904E PPQ 2.6 40.1 + - - +
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Residues in contact with LEU 322 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309E ASN* 5.1 1.3 - - - +
313E ASN* 3.8 17.5 - - - +
318E SER 3.5 10.9 + - - +
319E TYR* 3.8 39.2 + - + +
320E LYS 3.6 0.2 - - - -
321E ARG* 1.3 102.1 - - + +
323E VAL* 1.3 67.0 + - - +
328E ALA* 4.3 5.2 - - + -
329E PRO 4.2 18.4 - - - +
330E VAL* 3.7 19.9 - - + +
360E PHE* 3.9 13.9 - - + +
410E VAL* 4.1 21.1 - - + -
411E ALA 4.5 0.9 - - - +
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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