Contacts of the strand formed by residues 327 - 331 (chain D) in PDB entry 1F9E
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 PHE 327 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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262C THR* 3.2 38.4 - - + -
263C SER* 5.2 0.2 - - - -
265C PHE* 3.6 22.0 - - + -
266C THR* 4.0 12.6 - - + -
278C LYS* 3.5 30.5 - - + -
280C PHE* 3.9 21.8 - + - -
323D ASP 4.7 0.4 - - - -
324D GLU* 3.4 20.2 - - + +
325D ALA 3.2 20.6 - - - -
326D ASP* 1.3 74.8 - - - +
328D LEU* 1.3 62.2 + - - +
329D LEU* 4.2 2.2 - - + +
392D PHE* 3.4 3.1 - - - -
393D THR* 2.7 41.2 + - + +
394D LEU* 3.3 9.9 - - - +
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Residues in contact with LEU 328 (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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278C LYS 3.1 6.9 + - - +
279C VAL* 4.1 21.3 - - + -
280C PHE* 2.7 33.8 + - - +
281C PHE* 5.4 1.1 - - + -
327D PHE* 1.3 78.3 - - - +
329D LEU* 1.3 67.0 + - - +
330D GLY 5.0 0.2 - - - +
366D ILE* 3.3 48.2 - - + -
367D LEU* 4.9 3.1 - - + -
370D LEU* 4.0 16.8 - - + -
389D PRO* 4.7 4.0 - - + -
390D THR 3.6 11.9 - - - +
392D PHE* 4.0 9.2 - - + -
394D LEU* 3.8 17.0 - - + -
398D LEU* 4.2 6.7 - - + -
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Residues in contact with LEU 329 (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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258C ILE* 4.1 20.6 - - + -
262C THR* 4.9 9.6 - - + -
280C PHE* 3.2 24.2 - - + +
282C ILE* 4.2 10.8 - - + -
327D PHE* 4.2 3.0 - - + +
328D LEU* 1.3 76.3 - - - +
330D GLY* 1.3 70.8 + - - +
331D MET* 3.8 33.5 + - + -
389D PRO* 3.3 2.8 - - - +
390D THR* 2.9 46.5 + - - +
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Residues in contact with GLY 330 (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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280C PHE 2.7 14.4 + - - -
281C PHE* 3.5 10.9 - - - -
282C ILE 3.0 24.6 + - - -
328D LEU* 4.0 3.4 + - - +
329D LEU* 1.3 75.8 - - - +
331D MET* 1.3 64.6 + - - -
349D TYR* 3.4 21.8 + - - -
370D LEU* 5.3 1.3 - - - -
389D PRO* 4.4 9.2 - - - -
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Residues in contact with MET 331 (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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258C ILE* 3.4 30.1 - - + -
282C ILE* 3.8 25.6 - - + +
284C ALA 6.0 0.2 - - - +
286C GLN* 3.5 33.2 - - + +
329D LEU* 3.8 26.0 - - + -
330D GLY* 1.3 74.5 - - - -
332D ALA* 1.3 60.4 + - - +
333D THR* 3.3 14.6 - - + +
349D TYR* 3.6 9.6 + - - -
387D PRO* 3.7 2.3 - - - +
388D GLN* 3.2 45.2 + - + +
389D PRO* 4.7 0.5 - - - +
390D THR* 5.6 1.6 - - - +
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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