Contacts of the strand formed by residues 325 - 332 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266E LYS* 3.7 9.0 - - - +
268E ILE* 3.3 49.4 - - + +
270E MSE 4.3 18.8 - - - -
317E TYR* 4.0 26.0 - - + -
318E VAL* 4.3 13.2 - - + +
322E ARG 4.2 7.9 - - - +
323E ARG* 3.5 16.9 - - - +
324E ASP* 1.3 79.9 - - + +
326E PHE* 1.3 67.6 + - - +
327E GLU* 6.0 0.2 - - + -
378E GLY 4.7 0.9 - - - +
379E VAL* 4.0 13.5 - - + +
380E PRO* 3.6 15.8 - - - +
301F PHE* 3.8 14.1 - - + -
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Residues in contact with PHE 326 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258E ARG* 4.2 13.2 - - + -
261E LEU* 3.7 22.0 - - + -
266E LYS* 3.8 28.5 - - + -
268E ILE 3.0 14.0 + - - -
269E GLU* 3.4 52.5 - - + -
270E MSE 2.9 26.9 + - - +
300E ILE* 4.1 18.8 - - + -
325E LEU* 1.3 76.2 - - - +
327E GLU* 1.3 66.9 + - - +
328E THR* 3.8 5.8 - - - -
379E VAL* 3.9 2.7 - - - -
380E PRO* 3.4 26.9 - - + +
382E LEU* 3.8 20.0 - - + -
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Residues in contact with GLU 327 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270E MSE 3.4 17.7 - - + +
272E ILE* 3.7 18.0 - - + +
307E PHE* 3.6 24.1 - - - -
318E VAL* 3.6 14.7 - - + +
325E LEU* 6.0 0.4 - - + -
326E PHE* 1.3 78.5 - - - +
328E THR* 1.3 58.6 + - - +
329E VAL* 4.0 2.0 - - + -
374E HIS* 2.9 34.6 + - - +
379E VAL* 3.7 7.5 - - + +
380E PRO 2.9 6.7 + - - +
381E ASN* 3.3 32.6 + - - +
382E LEU* 2.8 34.6 + - - +
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Residues in contact with THR 328 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7E PHE* 5.4 0.2 - - + -
254E TYR* 3.8 18.9 - - + +
269E GLU* 2.5 31.2 + - - +
270E MSE 3.0 6.8 + - - -
271E LEU* 3.4 22.7 - - + +
272E ILE 2.8 30.6 + - - +
326E PHE* 3.8 0.5 - - - -
327E GLU* 1.3 74.2 + - - +
329E VAL* 1.3 56.8 + - - +
382E LEU* 3.4 19.3 - - + +
384E VAL* 3.8 27.4 - - + -
401E PHE* 5.2 0.4 - - + -
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Residues in contact with VAL 329 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272E ILE* 3.5 22.0 - - + -
274E TYR* 3.8 18.8 - - + -
307E PHE* 6.2 0.4 - - + -
327E GLU* 4.6 2.9 - - + -
328E THR* 1.3 76.5 - - - +
330E LEU* 1.3 74.2 + - - +
331E LYS* 3.5 1.3 + - + -
367E TYR* 3.8 35.9 - - + -
371E LEU* 4.9 4.7 - - + -
381E ASN* 3.7 22.9 - - - +
382E LEU 2.8 18.0 + - - +
383E ILE* 3.6 5.3 - - + +
384E VAL 2.9 27.1 + - - +
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Residues in contact with LEU 330 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271E LEU* 3.9 39.3 - - + -
272E ILE 2.8 18.0 + - - +
273E ASN* 4.0 16.3 - - + +
274E TYR* 4.2 6.4 + - - +
278E LEU* 4.2 26.9 - - + +
281E PHE* 4.1 18.8 - - + -
282E ALA* 6.1 0.2 - - + -
329E VAL* 1.3 79.5 - - - +
331E LYS* 1.3 58.3 + - - +
332E VAL* 4.1 2.6 + - - +
384E VAL* 3.5 31.9 - - + -
386E ILE* 4.1 18.2 - - + -
397E LEU* 5.1 0.7 - - + -
401E PHE* 4.0 13.0 - - + -
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Residues in contact with LYS 331 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274E TYR* 5.6 6.5 - - + -
329E VAL 3.5 0.6 + - - +
330E LEU* 1.3 74.3 - - - +
332E VAL* 1.3 87.9 + - - +
333E GLY* 3.7 8.5 + - - +
360E ASP* 5.3 2.8 + - - -
363E ASN 5.8 0.2 - - - -
364E THR* 3.8 30.7 + - - +
367E TYR* 3.6 60.6 - - + +
383E ILE* 4.3 3.6 - - + -
384E VAL 3.0 10.2 + - - +
385E ASN* 3.6 20.1 - - - +
386E ILE* 2.9 27.8 + - - +
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Residues in contact with VAL 332 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275E GLU* 4.4 22.2 - - + +
278E LEU* 4.1 25.4 - - + -
330E LEU 4.1 1.7 + - - +
331E LYS* 1.3 97.3 + - - +
333E GLY* 1.3 64.3 + - - +
334E LYS 3.4 25.8 - - - +
335E SER* 5.1 2.9 - - - -
360E ASP* 5.3 3.8 - - - +
386E ILE* 3.1 16.2 - - + +
388E GLU* 4.2 10.5 - - - -
389E LEU* 4.1 24.7 - - + -
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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