Contacts of the helix formed by residues 422 - 433 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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311A LEU 3.8 20.9 - - - +
312A HIS* 5.5 1.6 - - - +
315A GLY 4.5 2.0 - - - -
316A GLN* 4.0 20.4 - - + +
291B GLU* 4.4 13.2 - - - +
419B GLN* 3.4 28.3 - - + +
421B GLY* 1.3 74.7 - - - +
423B GLU* 1.3 76.0 + - - +
424B ALA 3.3 0.7 - - - -
425B TYR* 3.3 23.7 - - + -
426B LYS* 3.3 36.3 - - - +
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Residues in contact with GLU 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419B GLN* 4.9 1.4 - - - +
420B PRO* 3.6 21.1 - - + +
421B GLY 3.2 1.4 - - - -
422B VAL* 1.3 92.4 - - + +
424B ALA* 1.3 57.3 + - - +
426B LYS* 3.4 20.3 + - - +
427B LYS* 2.9 32.8 + - - +
430B PHE* 6.1 0.3 - - - -
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Residues in contact with ALA 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319A GLN* 3.7 34.3 - - + +
373A ALA* 3.8 8.5 - - + -
420B PRO 4.7 1.0 + - - -
421B GLY 3.7 3.9 + - - +
422B VAL 3.3 1.2 - - - -
423B GLU* 1.3 76.3 - - - +
425B TYR* 1.3 65.4 + - - +
427B LYS* 3.9 9.3 - - - +
428B ASN* 3.3 27.9 + - - +
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Residues in contact with TYR 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308A SER* 5.7 0.7 - - - -
311A LEU* 3.8 37.2 + - + -
312A HIS* 3.3 34.3 + - - -
315A GLY* 5.8 2.2 - - - -
319A GLN* 4.7 2.3 + - - +
366A ALA* 5.9 0.7 - - + -
369A GLY 4.3 4.5 - - - -
370A THR* 3.5 38.6 - - + +
373A ALA* 3.7 12.0 - - + +
374A HIS* 5.2 4.0 - - - +
151B GLU* 4.5 5.1 + - - -
421B GLY 4.9 1.1 + - - -
422B VAL* 3.3 38.5 - - + +
424B ALA* 1.3 78.2 - - - +
426B LYS* 1.3 78.6 + - + +
428B ASN* 3.3 2.4 + - - +
429B MSE 2.8 51.0 + - + +
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Residues in contact with LYS 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A HIS* 4.8 11.2 + - - -
149B THR* 5.3 10.6 + - - +
422B VAL* 3.3 34.6 - - - +
423B GLU* 3.4 26.5 + - - +
424B ALA 3.3 0.4 - - - -
425B TYR* 1.3 113.7 - - + +
427B LYS* 1.3 63.3 + - - +
429B MSE 3.3 12.2 + - + +
430B PHE* 3.0 49.7 + - + -
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Residues in contact with LYS 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423B GLU 2.9 18.3 + - - +
424B ALA* 3.9 8.3 - - - +
426B LYS* 1.3 76.5 - - - +
428B ASN* 1.3 69.2 + - - +
430B PHE* 3.6 8.0 + - - +
431B ALA* 3.2 21.8 + - - +
438B PHE* 3.8 19.8 - - + -
441B LEU* 3.7 22.9 - - + -
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Residues in contact with ASN 428 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369A GLY* 3.1 35.1 + - - +
372A LEU* 4.0 10.3 - - - +
373A ALA* 3.4 23.6 - - - +
376A ASP* 5.2 2.8 + - - -
424B ALA 3.3 9.4 + - - +
425B TYR 3.7 3.8 - - - +
426B LYS 3.3 0.2 - - - -
427B LYS* 1.3 77.8 - - - +
429B MSE 1.3 66.6 + - - +
431B ALA* 3.3 2.1 + - - +
432B LEU* 2.9 28.6 + - - +
441B LEU* 3.9 11.7 - - - +
445B LEU* 3.6 29.4 - - + +
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Residues in contact with MSE 429 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A SER* 6.5 0.2 - - - -
362A VAL* 5.1 2.7 - - - +
365A LYS* 4.2 12.1 - - - +
366A ALA* 3.8 39.0 - - - +
369A GLY* 4.3 1.5 - - - -
121B ILE* 4.9 9.4 - - - -
150B THR* 3.6 32.3 - - + +
151B GLU* 5.7 4.5 - - - +
425B TYR* 2.8 33.3 + - + +
426B LYS* 3.3 12.8 + - + +
428B ASN* 1.3 77.0 - - - +
430B PHE* 1.3 76.2 + - + +
432B LEU* 3.1 2.8 + - - +
433B LEU* 2.8 49.3 + - + +
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Residues in contact with PHE 430 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353A TYR* 4.4 7.2 - - - -
148B THR 5.7 4.3 - - - -
150B THR* 3.6 23.8 - - - -
423B GLU* 6.1 0.4 - - - -
426B LYS* 3.0 45.1 + - + +
427B LYS* 4.0 5.2 - - - +
429B MSE 1.3 87.7 - - + +
431B ALA* 1.3 62.7 + - - +
433B LEU* 3.3 8.1 + - + +
434B GLY 3.3 4.0 + - - -
435B LYS* 2.9 67.8 + - + +
438B PHE* 4.1 23.1 - + + -
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Residues in contact with ALA 431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427B LYS 3.2 12.7 + - - +
428B ASN 3.5 7.9 - - - +
429B MSE 3.2 0.2 - - - -
430B PHE* 1.3 78.0 - - - +
432B LEU* 1.3 58.0 + - - +
434B GLY* 3.0 16.8 + - - -
438B PHE* 3.4 35.1 - - + +
441B LEU* 3.8 15.3 - - + -
442B LYS* 3.1 33.9 - - - +
445B LEU* 4.1 2.2 - - + -
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Residues in contact with LEU 432 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361A PHE* 4.4 4.5 - - - -
365A LYS* 3.8 29.3 - - + +
368A GLU* 3.8 19.3 - - + +
369A GLY* 3.5 36.1 - - - +
372A LEU* 5.0 1.1 - - + -
428B ASN 2.9 15.6 + - - +
429B MSE 3.8 3.4 - - - +
431B ALA* 1.3 75.9 - - - +
433B LEU* 1.3 60.1 + - - +
434B GLY 3.1 1.3 + - - -
442B LYS* 3.9 16.0 + - + +
445B LEU* 3.8 26.7 - - + -
446B GLU* 3.7 34.7 - - + +
449B LEU* 4.4 9.4 - - + -
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Residues in contact with LEU 433 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353A TYR* 3.5 35.2 - - + +
354A LEU* 3.8 21.2 - - + +
361A PHE* 3.8 31.8 - - + -
362A VAL* 3.9 27.8 - - + -
365A LYS* 3.8 17.5 - - + -
150B THR* 5.2 4.9 - - + -
429B MSE 2.8 39.7 + - + +
430B PHE* 3.7 12.6 - - + +
431B ALA 3.2 0.4 - - - -
432B LEU* 1.3 75.6 - - - +
434B GLY* 1.3 60.2 + - - +
435B LYS 3.5 0.2 - - - -
442B LYS* 4.8 0.2 - - - -
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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