Contacts of the strand formed by residues 416 - 423 (chain A) in PDB entry 1FO4
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 GLU 416 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322A GLN* 2.9 21.3 + - - +
325A GLU* 3.6 1.7 - - - +
411A TYR 4.5 2.1 - - - +
412A SER* 3.3 15.5 + - - +
413A ARG* 2.8 66.6 + - - +
414A GLU 3.0 1.0 - - - -
415A ASP* 1.3 79.1 - - - +
417A PHE* 1.3 64.0 + - - +
418A PHE* 6.4 0.2 - - + -
439A ARG* 2.6 38.4 + - + +
440A VAL 3.3 13.0 - - - +
441A LEU* 3.9 11.9 - - + -
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Residues in contact with PHE 417 (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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322A GLN* 3.6 22.9 - - - -
325A GLU* 3.4 12.3 - - - +
415A ASP* 4.1 16.2 - - - -
416A GLU* 1.3 78.8 - - - +
418A PHE* 1.3 62.9 + - - +
439A ARG* 3.4 6.8 - - - +
440A VAL* 2.9 38.0 + - + +
442A PHE* 3.8 26.0 - + - -
519A PHE* 4.3 1.9 - - + -
523A VAL* 4.1 14.4 - - + -
526A LYS* 3.6 48.5 - - + +
527A LEU* 3.7 31.9 - - + -
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Residues in contact with PHE 418 (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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325A GLU* 2.9 42.8 + - + +
326A VAL* 4.0 20.9 - - + +
328A ARG* 6.0 0.5 - - - +
329A GLY* 4.1 12.5 + - - -
364A VAL* 3.7 40.6 - - + -
367A ALA* 3.8 11.4 - - + -
368A SER* 4.0 14.4 - - - -
417A PHE* 1.3 75.8 - - - +
419A SER* 1.3 89.2 + - - +
420A ALA* 4.4 2.2 - - + -
437A GLY* 4.3 0.2 - - - -
438A MET 3.1 23.6 - - - -
439A ARG* 3.3 24.7 - - + -
519A PHE* 4.3 2.2 - - - -
526A LYS* 3.2 19.0 + - - -
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Residues in contact with SER 419 (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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329A GLY* 5.4 1.6 - - - -
418A PHE* 1.3 85.5 + - - +
420A ALA* 1.3 59.7 + - - +
421A PHE* 3.8 26.9 - - - -
438A MET* 2.7 36.2 + - - +
519A PHE* 3.4 27.6 - - - -
522A THR* 4.3 17.8 - - - +
526A LYS* 4.5 0.9 + - - -
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Residues in contact with ALA 420 (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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329A GLY* 3.3 37.2 - - - +
332A GLU* 4.2 20.0 - - + +
333A GLN* 3.9 13.7 - - + -
364A VAL* 3.9 7.4 - - + -
418A PHE* 4.4 0.4 - - + -
419A SER* 1.3 76.6 - - - +
421A PHE* 1.3 71.7 + - - +
436A CYS* 3.4 14.8 - - - +
548A LEU* 5.1 0.3 - - - +
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Residues in contact with PHE 421 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A GLU* 5.5 2.7 - - - -
333A GLN* 3.5 7.8 + - - -
419A SER* 3.8 31.2 - - - -
420A ALA* 1.3 83.4 - - - +
422A LYS* 1.3 61.7 + - - +
435A THR* 3.4 2.1 - - - -
436A CYS* 3.0 44.0 + - - -
438A MET* 4.8 1.8 - - - -
515A PHE* 3.7 53.4 - + + -
518A LYS* 3.9 31.2 - - + -
519A PHE* 4.1 7.6 - - + -
522A THR* 4.8 4.0 - - - -
546A THR* 6.0 2.5 - - - -
548A LEU* 4.0 24.2 - - + -
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Residues in contact with LYS 422 (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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332A GLU* 5.7 1.6 + - - -
333A GLN* 3.4 16.3 + - - +
336A TRP* 2.8 52.9 + - + -
360A ASP* 3.1 38.7 + - - +
421A PHE* 1.3 76.9 - - - +
423A GLN* 1.3 70.6 + - - +
424A ALA* 4.4 6.9 + - + -
427A ARG 5.6 2.5 - - - -
430A ASP* 2.9 29.1 + - - +
431A ILE 4.5 0.4 - - - -
432A ALA* 4.0 17.7 - - + +
434A VAL 3.8 5.6 - - - -
435A THR* 4.1 2.9 - - - +
515A PHE* 4.1 3.2 - - - -
1168A THR* 6.1 0.2 - - - +
3006A FAD 3.1 4.8 + - - -
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Residues in contact with GLN 423 (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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422A LYS* 1.3 79.5 - - - +
424A ALA* 1.3 88.7 + - - +
425A SER 5.0 1.2 + - - -
426A ARG 6.1 0.6 - - - -
432A ALA 3.8 0.3 - - - -
433A LYS* 2.8 27.8 + - - +
434A VAL 3.1 9.7 + - - +
507A PHE* 4.0 4.3 - - + -
511A LEU* 3.9 21.1 - - + -
515A PHE* 3.7 19.1 - - + -
1168A THR* 3.3 42.0 + - + +
1170A ASP* 3.7 18.4 + - - +
1302A PRO* 3.6 17.2 - - - +
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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