Contacts of the helix formed by residues 424 - 434 (chain A) in PDB entry 1F4L
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 ALA 424 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420A THR 3.4 8.0 + - - +
421A PHE 3.3 12.2 + - - +
422A THR 3.2 1.6 - - - -
423A ASP* 1.3 76.5 - - - +
425A ALA* 1.3 64.7 + - - +
426A GLU 3.2 1.8 - - - -
427A VAL* 3.1 17.1 - - + +
428A ILE* 3.1 29.5 + - + +
443A GLU* 5.5 1.1 - - + +
447A LEU* 3.8 26.0 - - + -
490A TYR* 4.0 1.1 - - - -
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Residues in contact with ALA 425 (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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41A ARG* 5.6 0.3 + - - -
422A THR 3.2 12.7 + - - +
423A ASP 3.1 2.6 - - - -
424A ALA* 1.3 77.2 - - - +
426A GLU* 1.3 57.2 + - - +
428A ILE* 4.7 0.2 - - - -
429A GLY* 2.8 27.9 + - - -
490A TYR* 3.3 32.6 + - + +
512A TRP* 3.5 23.7 - - - +
515A ILE* 4.1 10.1 - - + -
516A GLN* 5.8 2.2 - - - +
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Residues in contact with GLU 426 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A ARG* 6.2 1.3 - - - +
423A ASP 4.1 10.4 + - - +
424A ALA 3.2 0.6 - - - -
425A ALA* 1.3 78.0 - - - +
427A VAL* 1.3 59.1 + - + +
429A GLY* 3.9 0.6 - - - -
430A GLU* 2.8 56.7 + - - +
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Residues in contact with VAL 427 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A ASP 5.1 1.3 + - - +
424A ALA* 3.1 25.8 - - + +
426A GLU* 1.3 81.8 - - + +
428A ILE* 1.3 63.9 + - + +
430A GLU* 3.2 14.7 + - + +
431A ALA* 3.1 22.9 + - + +
439A LYS* 5.8 4.9 - - + -
443A GLU* 3.1 34.8 - - + +
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Residues in contact with ILE 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* 3.1 18.5 + - + +
425A ALA* 3.9 4.3 - - - +
427A VAL* 1.3 77.7 - - + +
429A GLY* 1.3 66.4 + - - +
431A ALA* 3.0 8.5 + - - +
432A TRP* 2.9 42.1 + - + +
440A ALA* 4.2 6.2 - - + +
443A GLU* 3.9 24.0 - - + -
444A ILE* 3.8 22.7 - - + -
447A LEU* 4.0 14.8 - - + -
490A TYR* 3.6 44.2 - - + -
512A TRP* 4.2 2.7 - - + -
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Residues in contact with GLY 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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37A TYR* 3.2 35.1 + - - -
41A ARG* 4.9 1.8 - - - -
425A ALA 2.8 17.1 + - - -
426A GLU 4.0 0.7 - - - -
428A ILE* 1.3 76.6 - - - +
430A GLU* 1.3 56.8 + - - +
432A TRP* 4.3 0.9 - - - -
433A GLU* 2.9 27.4 + - - +
512A TRP* 3.7 10.0 - - - -
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Residues in contact with GLU 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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426A GLU* 2.8 53.8 + - - +
427A VAL* 3.2 12.6 - - + +
429A GLY* 1.3 76.3 - - - +
431A ALA* 1.3 58.3 + - - +
433A GLU* 3.4 6.7 + - - +
434A SER* 2.9 31.9 + - - -
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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 VAL* 3.1 13.0 + - + +
428A ILE* 3.0 9.9 + - - +
430A GLU* 1.3 74.4 - - - +
432A TRP* 1.3 66.9 + - - +
434A SER* 3.4 6.8 + - - -
435A ARG 3.2 2.4 + - - -
436A GLU* 2.9 47.8 + - + +
439A LYS* 4.4 11.9 - - + -
440A ALA* 3.7 19.1 - - + +
443A GLU* 6.1 0.2 - - + -
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Residues in contact with TRP 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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33A VAL* 4.1 11.0 - - + -
34A TRP* 3.2 17.9 - - - -
37A TYR* 3.6 45.3 - + + -
360A THR* 3.7 23.6 - - + -
428A ILE* 2.9 26.7 + - + +
429A GLY 3.8 2.9 - - - +
431A ALA* 1.3 76.1 - - - +
433A GLU* 1.3 64.7 + - - +
435A ARG 3.1 9.9 + - - -
437A PHE* 3.5 31.5 - + + -
440A ALA* 3.7 22.7 - - + -
441A VAL* 4.2 9.0 - - + -
444A ILE* 3.8 15.0 - - + -
490A TYR 3.0 28.4 + - - -
491A LEU* 4.9 0.2 - - + -
493A PRO* 4.5 5.6 - - + +
494A VAL* 3.4 26.9 - - + -
512A TRP* 4.2 8.0 - + - -
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Residues in contact with GLU 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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5A LYS* 4.9 14.0 + - - -
34A TRP* 2.9 29.5 + - - +
37A TYR* 3.9 14.5 + - + +
38A GLN* 3.0 28.4 + - - +
43A HIS* 5.7 1.4 - - - -
429A GLY 2.9 17.1 + - - +
430A GLU* 3.7 8.7 - - - +
432A TRP* 1.3 78.6 - - - +
434A SER* 1.3 59.9 + - - +
435A ARG* 3.3 3.3 + - - +
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Residues in contact with SER 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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365A SER* 3.5 15.8 - - - -
430A GLU 2.9 20.3 + - - -
431A ALA* 3.4 6.1 + - - -
433A GLU* 1.3 76.1 - - - +
435A ARG* 1.3 77.1 + - - +
436A GLU* 3.1 22.8 + - - +
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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