Contacts of the helix formed by residues 317 - 322 (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 ASN 317 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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256D MET* 3.6 18.1 - - + +
257D PRO* 3.1 13.5 - - + +
258D LYS* 2.5 53.8 + - - +
315D THR* 3.6 7.6 - - - +
316D THR* 1.3 79.4 + - - +
318D SER* 1.3 56.5 + - - +
320D LYS* 2.7 32.3 + - - +
321D ARG 3.5 2.6 + - - -
457J PRO* 4.2 5.3 - - - +
461J GLU* 2.8 31.5 + - + +
465J TYR* 4.2 13.2 - - + -
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Residues in contact with SER 318 (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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257D PRO* 3.7 7.2 - - - +
313D ASN* 3.5 25.6 - - - -
314D PRO* 3.9 0.5 - - - +
315D THR* 2.5 37.4 + - - -
317D ASN* 1.3 73.0 - - - +
319D TYR* 1.3 58.7 + - - +
320D LYS 3.2 0.2 - - - -
321D ARG* 3.3 23.2 + - - +
322D LEU* 3.5 12.1 + - - +
362D ASP* 2.7 38.2 + - - +
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Residues in contact with TYR 319 (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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309D ASN* 3.8 4.2 - - + +
313D ASN* 2.9 31.4 + - + +
315D THR 3.1 28.5 - - - -
316D THR* 3.4 9.9 - - - +
317D ASN 3.0 0.8 - - - -
318D SER* 1.3 74.9 - - - +
320D LYS* 1.3 60.2 + - + +
321D ARG 3.2 1.6 - - - -
322D LEU* 3.8 37.6 + - + +
323D VAL* 4.4 5.0 - - - +
411D ALA* 3.4 27.6 - - + -
412D GLY 3.9 14.9 - - - +
413D SER* 3.1 20.6 - - - -
414D LEU* 3.4 27.9 - - + +
417D ALA* 3.0 24.6 - - - +
454J ARG* 4.9 7.5 + - - +
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Residues in contact with LYS 320 (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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258D LYS* 3.7 27.6 - - + +
316D THR* 3.8 10.3 + - - +
317D ASN* 2.7 13.7 + - - +
319D TYR* 1.3 79.2 - - + +
321D ARG* 1.3 59.7 + - - +
323D VAL* 3.6 17.9 - - - +
453D VAL* 4.4 12.3 - - - +
458D HIS* 5.3 1.0 + - - -
453J VAL 4.1 6.8 + - - -
454J ARG* 3.4 22.6 + - - +
455J MET* 3.4 26.1 - - - +
456J THR 3.3 26.2 + - - -
457J PRO* 4.2 2.5 - - + -
458J HIS* 4.4 5.0 - - - +
461J GLU* 3.0 37.7 + - - +
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Residues in contact with ARG 321 (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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257D PRO* 4.0 13.7 - - + +
258D LYS* 3.9 26.3 + - + +
265D GLY* 4.3 4.0 - - - -
266D SER 3.3 22.1 + - - -
267D GLY* 3.6 8.8 - - - -
317D ASN 3.5 1.4 + - - +
318D SER 3.3 10.5 + - - +
319D TYR 3.2 0.2 - - - -
320D LYS* 1.3 78.9 - - - +
322D LEU* 1.3 71.2 + - - +
323D VAL* 2.8 22.0 + - - +
326D TYR* 5.1 0.7 - - - +
328D ALA* 3.2 22.2 - - + +
329D PRO* 5.2 0.2 - - - +
359D ARG* 3.3 23.6 + - - +
360D PHE* 3.1 20.6 + - - +
361D PRO 3.5 9.4 + - - -
362D ASP* 3.7 13.9 + - - +
5903D PPQ 2.6 40.7 + - - +
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Residues in contact with LEU 322 (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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309D ASN* 5.1 1.3 - - - +
313D ASN* 3.8 17.5 - - - +
318D SER 3.5 11.4 + - - +
319D TYR* 3.8 39.5 + - + +
320D LYS 3.6 0.4 - - - -
321D ARG* 1.3 102.8 - - + +
323D VAL* 1.3 67.7 + - - +
328D ALA* 4.3 4.5 - - + -
329D PRO 4.2 17.7 - - - +
330D VAL* 3.7 19.6 - - + +
360D PHE* 3.9 14.1 - - + +
410D VAL* 4.1 20.9 - - + -
411D ALA 4.5 0.7 - - - +
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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