Contacts of the helix formed by residues 422 - 434 (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 VAL 422 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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291A GLU* 4.3 14.8 - - - +
419A GLN* 3.3 27.6 - - + +
421A GLY* 1.3 74.3 - - - +
423A GLU* 1.3 79.4 + - - +
424A ALA 3.3 0.4 - - - -
425A TYR* 3.3 22.9 - - + -
426A LYS* 3.3 36.4 - - - +
311B LEU 3.9 20.4 - - - +
312B HIS* 5.5 0.7 - - - -
315B GLY 4.5 1.6 - - - -
316B GLN* 4.0 20.0 - - + +
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Residues in contact with GLU 423 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419A GLN 4.9 1.2 - - - +
420A PRO* 3.7 21.1 - - + +
421A GLY 3.2 1.4 - - - -
422A VAL* 1.3 93.5 - - + +
424A ALA* 1.3 57.6 + - - +
426A LYS* 3.3 17.7 + - - +
427A LYS* 2.9 36.2 + - + +
430A PHE* 6.1 0.9 - - - -
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Residues in contact with ALA 424 (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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420A PRO 4.8 0.4 + - - -
421A GLY* 3.7 5.4 + - - +
422A VAL 3.3 1.2 - - - -
423A GLU* 1.3 77.8 - - - +
425A TYR* 1.3 64.2 + - - +
427A LYS* 3.5 10.2 + - - +
428A ASN* 3.2 26.6 + - - +
319B GLN* 3.9 23.8 - - + +
373B ALA* 3.8 17.9 - - + -
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Residues in contact with TYR 425 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A GLU* 4.3 4.9 + - - -
421A GLY 4.8 1.3 + - - -
422A VAL* 3.3 38.6 - - + -
423A GLU 3.5 0.2 - - - -
424A ALA* 1.3 77.9 - - - +
426A LYS* 1.3 80.2 + - + +
428A ASN* 3.3 1.9 + - - +
429A MSE 2.8 51.1 + - + +
308B SER* 5.6 0.9 - - - -
311B LEU* 3.7 36.5 + - + +
312B HIS* 3.2 34.8 + - - -
315B GLY* 5.8 2.5 - - - -
319B GLN* 4.7 2.3 + - - +
366B ALA* 5.3 1.1 - - + -
369B GLY 4.3 5.0 - - - -
370B THR* 3.4 38.4 - - + +
373B ALA* 3.6 12.2 - - + +
374B HIS* 5.2 3.8 - - - +
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Residues in contact with LYS 426 (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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149A THR* 5.2 8.4 + - - +
422A VAL* 3.3 37.8 + - - +
423A GLU* 3.3 22.4 + - - +
424A ALA 3.2 1.0 - - - -
425A TYR* 1.3 114.5 - - + +
427A LYS* 1.3 58.1 + - - +
429A MSE 3.2 11.1 + - + +
430A PHE* 2.8 55.2 + - + -
312B HIS* 4.6 13.4 + - - -
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Residues in contact with LYS 427 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A GLU* 2.9 19.3 + - + +
424A ALA* 3.9 9.4 - - - +
426A LYS* 1.3 75.1 - - - +
428A ASN* 1.3 66.3 + - - +
430A PHE* 3.4 11.9 + - - +
431A ALA* 3.0 23.6 + - - +
438A PHE* 4.1 19.6 - - + -
441A LEU* 3.3 23.8 - - + -
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Residues in contact with ASN 428 (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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424A ALA 3.2 8.6 + - - +
425A TYR 3.6 4.0 - - - +
426A LYS 3.2 0.6 - - - -
427A LYS* 1.3 77.4 - - - +
429A MSE 1.3 65.8 - - - +
431A ALA* 3.3 3.6 + - - +
432A LEU* 3.0 26.7 + - - +
441A LEU* 3.6 13.9 - - - +
445A LEU* 3.5 27.6 - - + +
369B GLY* 3.2 34.7 + - - +
372B LEU* 4.1 9.1 - - - +
373B ALA* 3.4 24.0 - - - +
376B ASP* 5.3 2.6 + - - -
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Residues in contact with MSE 429 (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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121A ILE* 4.7 6.7 - - - -
150A THR* 3.3 37.2 - - + +
151A GLU* 5.5 3.8 - - - +
425A TYR* 2.8 33.4 + - + +
426A LYS* 3.5 14.1 - - + +
428A ASN* 1.3 76.9 - - - +
430A PHE* 1.3 81.3 + - + +
432A LEU* 3.1 3.9 + - - +
433A LEU* 2.8 42.4 + - + +
308B SER* 6.4 0.2 - - - -
362B VAL* 5.0 1.6 - - - +
365B LYS 4.1 12.6 - - - +
366B ALA* 3.7 39.9 - - - +
369B GLY* 4.2 1.7 - - - -
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Residues in contact with PHE 430 (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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148A THR 5.7 3.6 - - - -
150A THR* 3.5 24.2 - - - -
423A GLU* 6.1 0.7 - - - -
426A LYS* 2.8 46.2 + - + +
427A LYS* 3.8 7.0 - - - +
429A MSE 1.3 81.6 - - + +
431A ALA* 1.3 63.0 + - - +
433A LEU* 3.3 11.0 + - + +
434A GLY 3.2 3.5 + - - -
435A LYS* 3.0 64.9 + - + +
438A PHE* 3.8 31.0 - + + -
353B TYR* 5.1 0.7 - - - -
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Residues in contact with ALA 431 (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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427A LYS 3.0 14.5 + - - +
428A ASN 3.5 9.0 - - - +
429A MSE 3.2 0.2 - - - -
430A PHE* 1.3 77.0 - - - +
432A LEU* 1.3 57.4 + - - +
434A GLY* 3.0 17.3 + - - -
438A PHE* 3.6 29.4 - - + +
441A LEU* 3.7 16.8 - - + -
442A LYS* 3.2 36.4 - - - +
445A LEU* 4.2 2.2 - - + -
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Residues in contact with LEU 432 (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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428A ASN 3.0 15.1 + - - +
429A MSE 3.8 3.1 - - - +
431A ALA* 1.3 76.0 - - - +
433A LEU* 1.3 60.8 + - - +
434A GLY 3.4 0.5 + - - -
442A LYS* 4.1 15.2 - - - +
445A LEU* 3.8 26.0 - - + -
446A GLU* 3.7 32.4 - - + +
449A LEU* 4.0 13.7 - - + -
361B PHE* 4.3 5.4 - - - -
365B LYS* 3.9 29.6 - - + +
368B GLU* 3.7 20.0 - - + +
369B GLY* 3.6 34.8 - - - +
372B LEU* 5.1 0.4 - - + -
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Residues in contact with LEU 433 (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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150A THR* 4.9 7.2 - - + -
429A MSE 2.8 38.0 + - + +
430A PHE* 3.7 12.8 - - + +
431A ALA 3.2 0.2 - - - -
432A LEU* 1.3 76.9 - - - +
434A GLY* 1.3 60.1 + - - +
442A LYS* 5.1 0.4 - - - -
353B TYR* 3.5 35.7 - - + +
354B LEU* 4.0 14.7 - - + +
357B GLU* 6.0 0.2 - - - +
361B PHE* 3.8 19.8 - - + -
362B VAL* 3.8 35.7 - - + +
365B LYS* 3.6 26.7 - - + -
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Residues in contact with GLY 434 (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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431A ALA 3.0 15.1 + - - -
432A LEU 3.1 1.4 - - - -
433A LEU* 1.3 79.6 - - - +
435A LYS* 1.3 65.5 + - - +
436A PRO* 3.3 5.4 - - - +
439A GLU* 5.3 2.8 - - - +
442A LYS* 4.2 16.8 - - - -
353B TYR* 3.6 12.0 - - - +
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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