Contacts of the helix formed by residues 422 - 434 (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 VAL 422 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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291E GLU* 4.3 11.7 - - - +
419E GLN* 3.2 28.0 - - + +
421E GLY* 1.3 77.0 - - - +
423E GLU* 1.3 77.0 + - - +
424E ALA 3.3 0.2 - - - -
425E TYR* 3.2 35.6 - - + -
426E LYS* 3.3 19.0 - - - +
311F LEU 3.8 20.6 - - - +
312F HIS* 5.6 0.4 - - - -
315F GLY 4.4 1.6 - - - -
316F GLN* 3.9 26.7 - - + +
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Residues in contact with GLU 423 (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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419E GLN 5.0 1.6 - - - +
420E PRO* 4.0 16.4 - - + +
421E GLY 3.2 1.2 - - - -
422E VAL* 1.3 87.9 - - + +
424E ALA* 1.3 64.5 + - - +
426E LYS* 3.2 39.4 + - - +
427E LYS* 3.0 35.3 + - - +
430E PHE* 5.7 2.1 - - - -
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Residues in contact with ALA 424 (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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420E PRO 4.8 0.8 + - - -
421E GLY* 3.7 6.2 + - - +
422E VAL 3.3 1.2 - - - -
423E GLU* 1.3 78.7 - - - +
425E TYR* 1.3 63.9 + - - +
427E LYS* 3.4 3.9 + - - +
428E ASN* 3.3 24.3 + - - +
319F GLN* 3.7 34.3 - - + +
373F ALA* 3.8 9.2 - - + -
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Residues in contact with TYR 425 (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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151E GLU* 4.3 6.5 + - - -
421E GLY 4.8 1.3 + - - -
422E VAL* 3.2 41.0 - - + -
423E GLU 3.5 0.2 - - - -
424E ALA* 1.3 78.7 - - - +
426E LYS* 1.3 76.4 + - + +
428E ASN* 3.3 2.8 + - - +
429E MSE 2.8 50.8 + - + +
308F SER* 5.6 1.1 - - - -
311F LEU* 3.7 38.9 + - + +
312F HIS* 3.3 32.6 + - - -
315F GLY* 6.1 1.8 - - - -
319F GLN* 4.7 2.6 + - - +
366F ALA* 5.8 1.1 - - + -
369F GLY 4.3 3.5 - - - -
370F THR* 3.5 39.3 - - + +
373F ALA* 3.6 13.3 - - + +
374F HIS* 5.3 4.0 - - - +
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Residues in contact with LYS 426 (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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149E THR* 5.5 7.9 + - - +
422E VAL* 3.3 28.1 + - - +
423E GLU* 3.2 40.4 + - - +
424E ALA 3.3 0.6 - - - -
425E TYR* 1.3 114.5 - - + +
427E LYS* 1.3 57.1 + - - +
429E MSE 3.2 13.3 + - + +
430E PHE* 2.8 53.9 + - + -
312F HIS* 4.8 11.6 + - - -
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Residues in contact with LYS 427 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423E GLU* 3.0 25.7 + - - +
424E ALA* 3.8 4.9 - - - +
426E LYS* 1.3 76.6 - - - +
428E ASN* 1.3 65.3 + - - +
430E PHE* 3.4 12.8 + - - +
431E ALA* 3.1 21.0 + - - +
438E PHE* 3.9 18.4 - - + -
441E LEU* 3.4 23.9 - - + +
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Residues in contact with ASN 428 (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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424E ALA 3.3 8.5 + - - +
425E TYR 3.3 4.8 + - - +
427E LYS* 1.3 78.0 - - - +
429E MSE 1.3 65.6 + - - +
431E ALA* 3.2 3.6 + - - +
432E LEU* 3.0 26.0 + - - +
441E LEU* 3.9 12.6 - - - +
445E LEU* 3.5 30.2 - - + +
369F GLY* 3.1 33.7 + - - +
372F LEU* 4.0 10.3 - - - +
373F ALA* 3.4 22.2 - - - +
376F ASP* 5.2 3.6 + - - -
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Residues in contact with MSE 429 (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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121E ILE* 4.9 6.5 - - - -
150E THR* 3.4 36.3 - - + +
151E GLU* 5.5 4.3 - - - +
425E TYR* 2.8 38.2 + - + +
426E LYS* 3.5 14.6 - - + +
428E ASN* 1.3 71.9 - - - +
430E PHE* 1.3 79.0 + - + +
432E LEU* 3.3 3.2 + - - +
433E LEU* 2.9 43.6 + - + +
308F SER* 6.5 0.2 - - - -
362F VAL* 5.0 2.0 - - - +
365F LYS* 4.2 10.3 - - - +
366F ALA* 3.6 42.6 - - - +
369F GLY* 4.3 1.0 - - - -
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Residues in contact with PHE 430 (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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148E THR 5.7 3.8 - - - -
150E THR* 3.6 24.2 - - - -
423E GLU* 5.7 2.0 - - - -
426E LYS* 2.8 46.3 + - + +
427E LYS* 3.7 6.7 - - - +
429E MSE 1.3 83.0 - - + +
431E ALA* 1.3 63.9 + - - +
433E LEU* 3.4 11.8 + - + +
434E GLY 3.4 3.3 + - - -
435E LYS* 3.0 68.4 + - + +
438E PHE* 3.9 26.7 - + + -
353F TYR* 4.8 1.3 - - - -
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Residues in contact with ALA 431 (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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427E LYS 3.1 13.8 + - - +
428E ASN 3.4 9.4 - - - +
430E PHE* 1.3 75.8 - - - +
432E LEU* 1.3 57.3 + - - +
434E GLY* 3.0 17.0 + - - -
438E PHE* 3.5 19.6 - - + +
441E LEU* 3.7 18.6 - - + -
442E LYS* 3.2 45.2 - - - +
445E LEU* 4.2 2.7 - - + -
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Residues in contact with LEU 432 (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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428E ASN 3.0 15.9 + - - +
429E MSE 3.9 2.9 - - - +
431E ALA* 1.3 77.0 - - - +
433E LEU* 1.3 59.8 + - - +
434E GLY 3.3 0.5 + - - -
442E LYS* 4.0 15.2 - - - +
445E LEU* 3.7 28.9 - - + -
446E GLU* 3.9 28.5 - - + +
449E LEU* 4.0 13.0 - - + -
361F PHE* 4.4 2.9 - - - -
365F LYS* 4.0 33.7 - - + +
368F GLU* 3.8 18.8 - - + +
369F GLY* 3.6 35.7 - - - +
372F LEU* 5.0 0.7 - - + -
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Residues in contact with LEU 433 (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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150E THR* 5.0 5.4 - - + -
429E MSE 2.9 41.3 + - + +
430E PHE* 3.7 12.1 - - + +
431E ALA 3.2 0.2 - - - -
432E LEU* 1.3 78.2 - - - +
434E GLY* 1.3 59.6 + - - +
442E LYS* 5.0 0.2 - - - -
353F TYR* 3.5 34.7 - - + +
354F LEU* 4.1 10.9 - - + +
361F PHE* 3.9 30.4 - - + -
362F VAL* 3.8 37.5 - - + -
365F LYS* 3.7 21.1 - - + -
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Residues in contact with GLY 434 (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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431E ALA 3.0 13.1 + - - -
432E LEU 3.1 1.0 - - - -
433E LEU* 1.3 80.0 - - - +
435E LYS* 1.3 65.3 + - - +
436E PRO* 3.4 6.6 - - - +
439E GLU* 5.5 0.7 - - - +
442E LYS* 3.9 18.4 - - - -
353F TYR* 3.8 9.4 - - - +
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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