Contacts of the strand formed by residues 325 - 332 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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266A LYS* 3.8 8.6 + - - +
268A ILE* 3.4 38.8 - - + +
270A MSE 4.4 16.8 - - - -
317A TYR* 4.1 13.9 - - + -
318A VAL* 4.0 23.6 - - + +
322A ARG 3.9 8.1 - - - +
323A ARG* 3.5 25.6 - - - +
324A ASP* 1.3 80.4 - - + +
326A PHE* 1.3 65.7 + - - +
378A GLY 4.6 0.9 - - - +
379A VAL* 3.9 14.5 - - + +
380A PRO* 3.5 15.6 - - - +
301B PHE* 3.8 20.9 - - + -
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Residues in contact with PHE 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258A ARG* 3.8 21.3 - - + -
261A LEU* 3.6 30.7 - - + -
266A LYS* 3.8 29.6 - - + -
268A ILE 3.0 13.2 + - - +
269A GLU* 3.4 53.1 - - + -
270A MSE 2.9 26.0 + - - +
300A ILE* 4.0 12.6 - - + -
325A LEU* 1.3 76.5 - - - +
327A GLU* 1.3 66.4 + - - +
328A THR* 3.9 5.6 - - - -
379A VAL* 4.0 2.2 - - - -
380A PRO* 3.5 18.6 - - + +
382A LEU* 3.9 19.5 - - + -
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Residues in contact with GLU 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270A MSE 3.4 17.0 - - + +
272A ILE* 3.6 17.4 - - + +
307A PHE* 3.5 25.4 - - - -
318A VAL* 3.7 12.9 - - + +
325A LEU* 5.9 0.2 - - + -
326A PHE* 1.3 78.5 - - - +
328A THR* 1.3 59.4 + - - +
329A VAL* 4.0 2.9 - - + -
374A HIS* 2.8 35.5 + - - +
379A VAL* 3.6 8.8 - - + +
380A PRO 2.9 7.8 + - - +
381A ASN* 3.3 31.4 + - - +
382A LEU* 2.8 33.6 + - - +
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Residues in contact with THR 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254A TYR* 3.8 15.6 - - + +
269A GLU* 2.7 27.8 + - - +
270A MSE 3.0 8.5 + - - -
271A LEU* 3.4 21.0 - - + +
272A ILE 2.8 26.1 + - - +
326A PHE* 3.9 0.7 - - - -
327A GLU* 1.3 73.8 + - - +
329A VAL* 1.3 64.2 + - - +
382A LEU* 3.4 26.1 - - + +
384A VAL* 3.8 27.8 - - + -
401A PHE* 5.3 0.4 - - + -
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Residues in contact with VAL 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272A ILE* 3.6 23.8 - - + +
274A TYR* 4.1 16.2 - - + -
307A PHE* 6.2 0.2 - - + -
327A GLU* 4.7 1.6 - - + -
328A THR* 1.3 76.7 - - - +
330A LEU* 1.3 74.7 + - - +
331A LYS* 3.4 2.8 + - + +
367A TYR* 3.7 36.6 - - + -
371A LEU* 5.0 3.6 - - + -
381A ASN* 3.9 22.0 - - - +
382A LEU 2.8 16.9 + - - +
383A ILE* 3.6 4.6 - - + +
384A VAL* 2.9 27.5 + - - -
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Residues in contact with LEU 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271A LEU* 4.0 24.9 - - + -
272A ILE 2.8 20.2 + - - +
273A ASN* 4.0 11.5 - - + +
274A TYR* 4.3 5.9 + - - +
278A LEU* 4.3 29.0 - - + +
281A PHE* 3.9 27.1 - - + -
282A ALA* 6.0 0.7 - - + -
329A VAL* 1.3 77.4 - - - +
331A LYS* 1.3 59.2 + - - +
332A VAL* 4.1 1.4 + - - +
384A VAL* 3.6 29.6 - - + -
386A ILE* 3.9 19.1 - - + -
401A PHE* 3.9 23.6 - - + -
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Residues in contact with LYS 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274A TYR* 5.5 7.6 - - + -
329A VAL* 3.4 1.5 + - + +
330A LEU* 1.3 72.4 - - - +
332A VAL* 1.3 83.8 + - - +
333A GLY* 3.7 7.3 + - - -
360A ASP* 5.7 1.8 + - - -
364A THR* 4.0 27.1 + - - +
367A TYR* 3.4 55.6 - - + +
383A ILE* 4.2 13.0 - - + -
384A VAL 3.1 7.5 + - - +
385A ASN* 3.6 21.0 - - - +
386A ILE* 2.8 29.1 + - - +
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Residues in contact with VAL 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275A GLU* 4.4 19.1 - - + +
278A LEU* 4.0 26.7 - - + -
330A LEU 4.1 1.1 + - - +
331A LYS* 1.3 93.3 + - - +
333A GLY* 1.3 66.1 + - - +
334A LYS 3.5 25.1 + - - +
335A SER* 5.4 1.3 - - - -
360A ASP* 5.5 2.8 - - - +
386A ILE* 3.1 15.5 - - + +
388A GLU* 4.1 13.0 - - - -
389A LEU* 4.1 27.1 - - + -
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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