Contacts of the helix formed by residues 314 - 321 (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 314 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286E LYS* 4.2 21.1 - - + +
290E GLY* 4.7 3.1 - - - -
301E PHE* 4.9 11.9 - - + -
302E PRO* 3.9 41.1 - - + +
270F MSE 4.2 20.0 - - + -
303F SER* 5.7 1.1 - - - +
304F SER 4.9 5.6 - - - +
305F ALA* 4.6 9.9 - - + -
307F PHE* 5.6 1.3 - - + -
310F ASP* 2.7 20.1 + - + +
313F SER* 1.3 84.9 + - - +
315F GLY* 1.3 57.5 + - - +
316F GLN 3.3 3.1 - - - -
317F TYR* 3.1 12.1 + - + +
318F VAL* 2.9 37.2 + - + +
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Residues in contact with GLY 315 (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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421E GLY 5.4 0.4 - - - -
422E VAL* 4.4 5.4 - - - -
425E TYR* 6.0 1.8 - - - -
307F PHE* 5.6 0.2 - - - -
310F ASP 3.0 7.3 + - - -
311F LEU* 3.4 38.1 + - - -
313F SER 3.6 0.6 - - - -
314F LEU* 1.3 77.3 - - - +
316F GLN* 1.3 62.1 + - - +
318F VAL* 3.4 6.7 + - - +
319F GLN* 3.0 25.6 + - - +
374F HIS* 4.6 2.8 + - - -
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Residues in contact with GLN 316 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291E GLU* 3.6 44.3 - - + +
294E GLY 3.0 29.4 + - - +
295E LYS* 4.1 11.0 - - - +
419E GLN* 3.0 23.4 - - + +
420E PRO* 4.1 2.7 - - - +
421E GLY* 2.7 26.1 + - - +
422E VAL* 3.8 16.1 + - + +
311F LEU 4.4 0.2 + - - -
313F SER 5.0 0.4 + - - -
314F LEU 3.3 0.6 - - - -
315F GLY* 1.3 74.6 - - - +
317F TYR* 1.3 56.8 + - - +
319F GLN* 3.3 3.7 + - - +
320F GLU* 2.9 51.7 + - - +
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Residues in contact with TYR 317 (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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290E GLY* 3.8 19.4 + - - +
293E GLU* 6.2 0.2 - - + -
294E GLY* 3.4 25.4 - - - -
298E LYS 4.0 6.3 - - - -
299E GLY 2.6 28.8 + - - -
300E ILE 3.4 21.8 - - - -
301E PHE* 3.6 39.3 + + - +
302E PRO* 4.4 7.6 - - + -
268F ILE* 5.9 0.2 - - - +
314F LEU* 3.1 16.3 + - + +
316F GLN* 1.3 77.1 - - - +
318F VAL* 1.3 69.3 + - + +
321F GLY 2.8 20.1 + - - +
322F ARG* 3.4 38.6 - - - +
323F ARG* 3.0 6.1 + - - -
325F LEU* 4.2 12.6 - - + +
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Residues in contact with VAL 318 (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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301E PHE* 5.9 0.7 - - + -
270F MSE 3.7 37.0 - - + -
307F PHE* 4.8 3.8 - - + -
314F LEU* 2.9 25.1 + - + +
315F GLY* 3.4 6.3 + - - +
317F TYR* 1.3 75.7 - - + +
319F GLN* 1.3 57.0 + - - +
323F ARG* 2.7 28.4 + - - -
325F LEU* 4.1 9.6 - - + -
327F GLU* 3.7 14.4 - - + +
374F HIS* 3.4 40.6 - - + +
379F VAL* 3.3 13.6 - - + +
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Residues in contact with GLN 319 (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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297E GLN* 4.9 1.9 + - - -
421E GLY* 3.3 24.9 - - - +
424E ALA* 3.7 22.4 - - + +
425E TYR* 4.7 1.9 + - - +
315F GLY 3.0 17.1 + - - +
316F GLN 3.7 2.7 - - - +
317F TYR 3.1 0.2 - - - -
318F VAL* 1.3 79.1 - - - +
320F GLU* 1.3 72.6 + - + +
323F ARG* 3.2 13.8 + - - +
373F ALA* 3.1 28.7 + - - +
374F HIS* 3.3 25.1 - - + +
376F ASP* 4.7 1.0 - - - +
377F GLY* 3.6 27.6 - - - +
379F VAL* 5.4 0.2 - - - -
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Residues in contact with GLU 320 (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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294E GLY 3.7 4.3 - - - +
295E LYS* 3.3 7.4 - - - -
296E ASP 4.4 7.3 + - - +
297E GLN* 2.7 43.7 + - - +
420E PRO* 3.7 15.1 - - - +
421E GLY* 3.3 23.3 + - - -
316F GLN* 2.9 37.3 + - - +
319F GLN* 1.3 89.2 - - + +
321F GLY* 1.3 57.7 + - - +
323F ARG* 4.4 0.9 - - - +
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Residues in contact with GLY 321 (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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294E GLY* 3.7 11.9 + - - -
297E GLN* 3.2 12.9 - - - -
298E LYS 3.2 18.4 - - - -
317F TYR* 2.8 24.9 + - - -
320F GLU* 1.3 74.6 - - - +
322F ARG* 1.3 67.1 + - - -
323F ARG* 2.9 13.4 + - - +
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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