Contacts of the strand formed by residues 325 - 332 (chain F) in PDB entry 3IFS
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 LEU 325 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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301E PHE* 4.0 16.2 - - + -
266F LYS* 3.6 9.7 - - - +
268F ILE* 3.3 43.3 - - + +
270F MSE 4.2 18.4 - - - -
317F TYR* 4.2 14.4 - - + +
318F VAL* 4.1 22.7 - - + +
322F ARG* 3.8 11.2 - - + +
323F ARG* 3.5 22.7 - - - +
324F ASP* 1.3 81.1 - - + +
326F PHE* 1.3 65.0 + - - +
378F GLY 4.6 1.2 - - - +
379F VAL* 3.8 13.8 - - + +
380F PRO* 3.5 18.5 - - - +
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Residues in contact with PHE 326 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258F ARG* 4.2 12.6 - - + -
261F LEU* 3.6 31.6 - - + -
266F LYS* 3.7 27.1 - - + -
268F ILE 3.0 11.7 + - - +
269F GLU* 3.4 52.7 - - + -
270F MSE 2.9 26.2 + - - +
300F ILE* 4.1 24.2 - - + -
325F LEU* 1.3 75.2 - - - +
327F GLU* 1.3 66.9 + - - +
328F THR* 3.8 7.0 - - - -
379F VAL* 4.0 2.0 - - - -
380F PRO* 3.5 19.5 - - + +
382F LEU* 3.9 18.2 - - + -
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Residues in contact with GLU 327 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270F MSE 3.4 17.3 - - + +
272F ILE* 3.6 19.4 - - + +
307F PHE* 3.5 23.2 - - - -
318F VAL* 3.8 11.9 - - + +
325F LEU* 5.9 0.2 - - + -
326F PHE* 1.3 79.4 - - - +
328F THR* 1.3 63.4 + - - +
329F VAL* 4.0 2.2 - - + -
374F HIS* 2.7 37.2 + - - +
379F VAL* 3.6 7.9 - - + +
380F PRO 2.9 7.0 + - - +
381F ASN* 3.3 31.9 + - - +
382F LEU* 2.8 26.9 + - - +
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Residues in contact with THR 328 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254F TYR* 3.8 17.4 - - + +
269F GLU* 2.6 28.4 + - - +
270F MSE 3.0 7.7 + - - -
271F LEU* 3.4 23.9 - - + +
272F ILE 2.8 23.7 + - - -
326F PHE* 3.8 1.2 - - - -
327F GLU* 1.3 74.3 + - - +
329F VAL* 1.3 61.2 + - - +
382F LEU* 3.4 25.2 - - + +
384F VAL* 3.9 27.1 - - + -
401F PHE* 5.2 0.4 - - + -
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Residues in contact with VAL 329 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272F ILE* 3.6 25.1 - - + +
274F TYR* 4.1 14.8 - - + -
327F GLU* 4.6 2.5 - - + -
328F THR* 1.3 74.5 - - - +
330F LEU* 1.3 71.7 + - - +
331F LYS* 3.4 1.9 + - + +
367F TYR* 3.7 36.8 - - + -
371F LEU* 4.9 3.4 - - + -
381F ASN* 3.7 23.3 - - - +
382F LEU 2.8 16.3 + - - +
383F ILE* 3.5 5.5 - - + +
384F VAL* 2.8 31.7 + - - +
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Residues in contact with LEU 330 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271F LEU* 4.0 23.8 - - + -
272F ILE 2.8 21.2 + - - +
273F ASN* 4.0 13.9 - - + +
274F TYR* 4.2 6.8 + - - +
278F LEU* 4.3 26.4 - - + +
281F PHE* 3.9 27.4 - - + -
282F ALA* 6.1 0.2 - - + -
329F VAL* 1.3 75.4 - - - +
331F LYS* 1.3 58.8 + - - +
332F VAL* 4.1 2.5 + - - +
384F VAL* 3.5 28.7 - - + -
386F ILE* 3.8 19.1 - - + -
397F LEU* 4.8 0.4 - - + -
401F PHE* 3.9 22.7 - - + -
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Residues in contact with LYS 331 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274F TYR* 5.5 7.2 - - + -
329F VAL* 3.4 1.3 + - + +
330F LEU* 1.3 73.3 - - - +
332F VAL* 1.3 85.0 + - - +
333F GLY* 3.8 6.5 + - - -
360F ASP* 5.6 1.4 + - - -
363F ASN 5.9 0.2 - - - -
364F THR* 3.9 27.9 + - - +
367F TYR* 3.3 56.8 - - + -
383F ILE* 4.2 10.8 - - + -
384F VAL 2.9 9.3 + - - +
385F ASN* 3.5 21.7 - - - +
386F ILE* 2.8 28.1 + - - +
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Residues in contact with VAL 332 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275F GLU* 4.6 16.4 - - + +
278F LEU* 4.2 19.3 - - + -
330F LEU 4.1 1.5 + - - +
331F LYS* 1.3 94.3 + - - +
333F GLY* 1.3 62.9 + - - +
334F LYS 3.3 28.1 - - - +
335F SER* 4.6 3.4 - - - +
360F ASP* 5.3 3.3 - - - +
386F ILE* 3.1 17.5 - - + +
388F GLU* 4.1 10.8 - - - -
389F LEU* 3.9 34.1 - - + -
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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