Contacts of the helix formed by residues 314 - 321 (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 314 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270E MSE 4.7 17.3 - - + -
303E SER* 5.7 0.7 - - - +
304E SER 5.3 4.3 - - - +
305E ALA* 5.3 5.6 - - + -
307E PHE* 5.8 1.3 - - + -
310E ASP* 2.7 16.6 + - + +
313E SER* 1.3 84.8 + - - +
315E GLY* 1.3 61.0 + - - +
316E GLN 3.2 2.7 - - - -
317E TYR* 3.0 11.5 + - + +
318E VAL* 2.8 37.5 + - + +
286F LYS* 3.9 26.5 - - + +
290F GLY* 4.3 5.4 - - - -
301F PHE* 4.8 14.1 - - + -
302F PRO* 3.8 41.1 - - + +
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Residues in contact with GLY 315 (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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307E PHE* 5.8 0.2 - - - -
310E ASP 3.1 6.9 + - - -
311E LEU* 3.4 37.6 + - - -
313E SER 3.6 0.2 - - - -
314E LEU* 1.3 77.7 - - - +
316E GLN* 1.3 61.7 + - - +
318E VAL* 3.5 5.9 + - - +
319E GLN* 3.0 25.5 + - - +
374E HIS* 4.5 3.2 + - - -
421F GLY 4.9 0.7 - - - +
422F VAL* 4.6 4.9 - - - -
425F TYR* 5.9 2.2 - - - -
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Residues in contact with GLN 316 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313E SER 5.0 0.4 + - - -
314E LEU 3.2 0.4 - - - -
315E GLY* 1.3 75.0 - - - +
317E TYR* 1.3 59.7 + - - +
319E GLN* 3.8 1.2 - - - +
320E GLU* 2.9 50.2 + - - +
291F GLU* 3.6 45.2 + - + +
294F GLY 2.9 26.7 + - - +
295F LYS* 3.1 14.7 - - - +
419F GLN* 3.0 22.0 - - + +
420F PRO* 4.1 0.6 - - - +
421F GLY* 2.7 28.9 + - - +
422F VAL* 3.8 15.5 + - + +
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Residues in contact with TYR 317 (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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314E LEU* 3.0 17.6 + - + +
316E GLN* 1.3 77.3 - - - +
318E VAL* 1.3 67.6 + - + +
321E GLY 2.8 20.0 + - - +
322E ARG* 3.4 29.0 - - - +
323E ARG* 3.0 6.2 + - - -
325E LEU* 4.0 18.1 - - + +
267F THR 4.9 0.2 + - - -
290F GLY* 3.8 18.9 + - - +
293F GLU* 5.3 0.4 - - + -
294F GLY* 3.5 28.7 - - - -
298F LYS 4.1 2.5 - - - -
299F GLY* 2.7 27.5 + - - -
300F ILE 3.5 21.5 - - - -
301F PHE* 3.6 38.4 + + - +
302F PRO* 4.3 8.5 - - + -
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Residues in contact with VAL 318 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270E MSE 3.7 37.2 - - + -
307E PHE* 4.9 4.9 - - + -
314E LEU* 2.8 28.3 + - + +
315E GLY* 4.0 5.2 - - - +
317E TYR* 1.3 73.1 - - + +
319E GLN* 1.3 55.5 + - - +
323E ARG* 2.8 26.8 + - - +
325E LEU* 4.3 9.0 - - + -
327E GLU* 3.6 15.0 - - + +
374E HIS* 3.5 37.9 - - + +
379E VAL* 3.3 13.7 - - + +
301F PHE* 5.9 0.2 - - + -
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Residues in contact with GLN 319 (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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315E GLY 3.0 18.6 + - - +
316E GLN 3.8 2.7 - - - +
318E VAL* 1.3 78.1 - - - +
320E GLU* 1.3 72.0 + - + +
323E ARG* 3.2 13.4 + - - +
373E ALA* 2.9 33.9 + - - +
374E HIS* 3.3 22.7 - - - +
376E ASP* 4.6 1.0 - - - +
377E GLY* 3.5 28.4 - - - +
379E VAL* 5.4 0.4 - - - -
297F GLN* 5.1 2.1 + - - -
421F GLY* 3.5 23.9 - - - +
424F ALA* 3.7 18.9 - - + +
425F TYR* 4.6 1.9 + - - +
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Residues in contact with GLU 320 (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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316E GLN* 2.9 35.3 + - - +
319E GLN* 1.3 91.2 - - + +
321E GLY* 1.3 58.2 + - - +
323E ARG* 4.6 0.4 - - - -
294F GLY 3.7 3.6 - - - +
295F LYS* 3.3 11.6 - - - +
296F ASP 4.5 4.6 + - - +
297F GLN* 2.7 44.0 + - - +
420F PRO* 3.5 17.0 - - - +
421F GLY* 3.4 24.4 + - - -
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Residues in contact with GLY 321 (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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317E TYR* 2.8 26.2 + - - -
320E GLU* 1.3 76.3 - - - +
322E ARG* 1.3 63.8 + - - -
323E ARG* 2.8 18.7 + - - +
294F GLY* 3.8 11.6 + - - -
297F GLN* 3.2 14.2 - - - -
298F LYS 3.3 15.3 - - - -
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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