Contacts of the helix formed by residues 317 - 322 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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457A PRO* 4.3 3.2 - - - +
461A GLU* 2.7 33.7 + - - +
465A TYR* 4.1 13.5 - - + -
256G MET* 3.6 18.9 - - + +
257G PRO* 3.1 13.4 - - + +
258G LYS* 2.5 53.7 + - - +
315G THR* 3.6 7.8 - - - +
316G THR* 1.3 80.1 + - - +
318G SER* 1.3 56.7 + - - +
320G LYS* 2.7 32.9 + - - +
321G ARG 3.5 3.1 + - - -
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Residues in contact with SER 318 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257G PRO* 3.7 6.2 - - - +
313G ASN* 3.5 24.3 - - - -
314G PRO* 3.9 0.7 - - - +
315G THR* 2.5 39.1 + - - +
317G ASN* 1.3 72.9 - - - +
319G TYR* 1.3 58.8 + - - +
321G ARG* 3.3 22.9 + - - +
322G LEU* 3.5 12.5 + - - +
362G ASP* 2.7 38.3 + - - +
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Residues in contact with TYR 319 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454A ARG* 4.9 8.3 + - - +
309G ASN* 3.8 4.0 - - + +
313G ASN* 2.9 30.9 + - + +
315G THR 3.1 26.7 - - - -
316G THR* 3.4 10.1 - - - +
317G ASN 3.0 0.4 - - - -
318G SER* 1.3 73.5 - - - +
320G LYS* 1.3 62.5 + - + +
321G ARG 3.2 2.9 + - - -
322G LEU* 3.8 36.6 + - + +
323G VAL* 4.4 4.5 - - - +
411G ALA* 3.4 27.6 - - + -
412G GLY 3.9 14.8 - - - +
413G SER* 3.1 22.4 - - - -
414G LEU* 3.4 28.9 - - + +
417G ALA* 3.0 25.3 - - - +
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Residues in contact with LYS 320 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453A VAL 4.1 6.5 + - - -
454A ARG* 3.3 27.1 + - - +
455A MET* 3.5 22.3 - - - +
456A THR 3.4 24.2 - - - -
457A PRO* 4.3 2.5 - - + -
458A HIS* 4.4 5.0 - - - +
461A GLU* 3.0 36.3 + - - +
258G LYS* 3.7 25.9 - - + +
316G THR* 3.8 10.9 + - - +
317G ASN* 2.7 14.5 + - - +
319G TYR* 1.3 79.2 - - - +
321G ARG* 1.3 59.5 + - - +
323G VAL* 3.6 17.9 - - - +
453G VAL* 4.4 12.9 - - - +
458G HIS* 5.3 1.0 + - - -
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Residues in contact with ARG 321 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257G PRO* 4.0 12.6 - - + +
258G LYS* 3.9 26.7 + - + +
265G GLY* 4.3 4.5 - - - -
266G SER 3.3 21.7 + - - -
267G GLY* 3.6 8.0 - - - -
268G MET 4.5 0.2 - - - +
317G ASN 3.5 1.4 + - - +
318G SER 3.3 10.8 - - - +
319G TYR 3.2 0.2 - - - -
320G LYS* 1.3 78.7 - - - +
322G LEU* 1.3 69.9 + - - +
323G VAL* 2.8 22.3 + - - +
326G TYR* 5.1 0.5 - - - +
328G ALA* 3.2 22.2 - - + +
329G PRO* 5.2 0.2 - - - +
359G ARG* 3.3 24.0 + - - +
360G PHE* 3.1 21.4 + - - +
361G PRO 3.5 8.4 + - - -
362G ASP* 3.7 12.9 + - - +
5906G PPQ 2.6 40.8 + - - +
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Residues in contact with LEU 322 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309G ASN* 5.1 1.6 - - - +
313G ASN* 3.8 17.3 - - - +
318G SER 3.5 11.2 + - - +
319G TYR* 3.8 40.3 + - + +
320G LYS 3.6 0.2 - - - -
321G ARG* 1.3 101.4 - - - +
323G VAL* 1.3 66.6 + - - +
328G ALA* 4.3 5.2 - - + -
329G PRO 4.2 17.9 - - - +
330G VAL* 3.7 20.1 - - + +
360G PHE* 3.9 14.6 - - + +
410G VAL* 4.1 21.8 - - + -
411G ALA 4.5 1.8 - - - +
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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