Contacts of the strand formed by residues 416 - 428 (chain A) in PDB entry 5FI4
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 LYS 416 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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411A GLY* 3.4 21.4 - - - +
413A LYS* 3.1 25.3 + - + +
414A GLY 3.2 1.7 - - - +
415A ALA* 1.3 75.9 - - - +
417A GLU* 1.3 61.8 + - - +
418A GLU* 4.3 1.1 + - - +
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Residues in contact with GLU 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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375A ARG* 3.0 43.3 + - - -
409A VAL* 3.8 8.1 - - + +
410A LYS 3.5 9.0 - - - +
411A GLY* 3.8 11.3 + - - -
415A ALA 3.6 7.7 + - - +
416A LYS* 1.3 74.0 - - - +
418A GLU* 1.4 65.4 + - - +
419A HIS* 3.5 20.6 + - - +
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Residues in contact with GLU 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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408A SER* 3.7 2.4 + - - +
409A VAL* 3.6 3.5 - - - -
410A LYS* 2.8 44.6 + - + +
411A GLY 5.0 0.6 + - - +
416A LYS 5.8 0.9 - - - +
417A GLU* 1.4 74.8 - - - +
419A HIS* 1.4 64.5 + - - +
420A CYS* 4.1 3.1 + - - -
568B PRO* 3.0 48.8 - - + +
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Residues in contact with HIS 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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355A TYR* 2.7 34.3 + + - +
372A ASN* 6.0 1.3 - - - -
375A ARG* 3.7 15.5 - - - -
407A CYS* 5.4 0.2 - - + -
408A SER 3.4 4.9 - - - +
409A VAL* 3.6 20.0 - - + +
417A GLU* 3.5 33.8 + - + +
418A GLU* 1.4 78.1 + - - +
420A CYS* 1.3 66.2 + - - +
421A PRO* 4.6 0.5 - - - +
453A GLU 4.9 2.8 - - - +
455A LEU* 3.4 31.1 - - + +
348B ARG* 5.9 0.5 + - - -
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Residues in contact with CYS 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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407A CYS* 3.2 2.3 - - - +
408A SER* 2.8 49.0 + - - +
418A GLU* 4.1 2.8 + - - -
419A HIS* 1.3 79.8 - - - +
421A PRO* 1.4 73.9 - - + +
422A LEU* 4.0 2.1 - - + +
453A GLU 6.1 0.2 - - - -
455A LEU* 4.0 3.6 - - - +
564B ASN* 5.1 2.9 - - - +
567B LYS* 4.1 13.0 - - + -
568B PRO* 3.5 49.1 - - + -
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Residues in contact with PRO 421 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405A SER* 4.7 3.8 - - - -
406A ILE 3.7 6.7 - - - +
407A CYS* 4.0 5.8 - - - -
420A CYS* 1.4 88.1 - - + +
422A LEU* 1.3 63.4 + - - +
424A TRP* 6.0 1.3 - - + -
448A VAL* 3.7 33.1 - - + +
452A LEU 4.7 2.9 - - - +
453A GLU* 3.8 12.6 - - - +
454A ASP 3.3 17.9 - - - +
455A LEU* 3.4 34.5 - - + +
564B ASN* 4.3 0.2 - - - +
567B LYS* 3.9 18.1 + - - -
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Residues in contact with LEU 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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344A VAL* 3.5 39.0 - - + -
345A ASN 6.0 0.9 - - - +
346A VAL* 3.8 15.7 - - + -
354A ILE* 3.8 21.1 - - + -
406A ILE* 2.8 29.4 + - + +
408A SER* 3.6 30.1 - - - +
420A CYS* 4.0 2.0 - - + +
421A PRO* 1.3 77.9 - - - +
423A ALA* 1.3 60.5 - - + +
447A PRO* 5.0 2.3 - - - +
448A VAL* 3.8 12.2 + - - +
560B ASP* 5.1 7.3 - - - +
564B ASN* 3.9 31.2 + - + +
567B LYS* 5.3 1.6 + - - -
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Residues in contact with ALA 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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344A VAL* 6.1 1.1 - - + -
405A SER* 3.3 5.6 - - - -
406A ILE* 3.1 28.4 + - + +
421A PRO 3.8 0.2 - - - -
422A LEU* 1.3 79.9 - - + +
424A TRP* 1.3 60.3 + - - +
445A LEU* 3.6 29.7 - - + +
446A TRP 3.3 17.9 - - - +
447A PRO* 5.3 0.4 - - + -
448A VAL* 3.8 5.6 - - - +
471A PRO* 4.7 16.2 - - + -
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Residues in contact with TRP 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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404A LEU 3.5 12.6 - - - +
405A SER* 4.2 6.7 - - - +
421A PRO* 6.0 1.1 - - + -
423A ALA* 1.3 74.1 - - - +
425A GLY* 1.3 72.5 + - - +
426A ASN* 3.5 24.7 - - - -
445A LEU* 3.4 9.9 - - - -
446A TRP* 2.8 75.7 + + + +
447A PRO 2.9 25.1 + - - -
448A VAL* 3.9 13.7 - - + -
449A PRO* 3.8 10.0 - - + +
455A LEU 5.4 0.9 - - - +
456A LEU 5.5 0.2 - - - -
457A ASN* 3.4 35.8 - - + +
460A GLY* 3.6 6.3 - - - -
461A VAL* 3.3 46.9 - - + -
679A THR* 5.0 6.5 - - + -
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Residues in contact with GLY 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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404A LEU* 2.8 36.2 + - - +
424A TRP* 1.3 84.2 - - - +
426A ASN* 1.3 64.6 + - - +
443A LEU* 4.1 11.2 - - - -
444A ASN 5.5 0.4 - - - -
445A LEU* 3.9 15.1 - - - +
446A TRP* 4.5 6.1 - - - -
463A GLY 5.5 0.9 - - - -
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Residues in contact with ASN 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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401A ARG* 3.3 11.8 - - - +
402A LEU 3.3 7.9 - - - +
403A CYS* 3.4 22.3 - - - +
404A LEU 3.9 2.3 + - - +
424A TRP* 3.5 14.9 - - - -
425A GLY* 1.3 90.0 + - - +
427A ILE* 1.3 62.8 + - - +
443A LEU* 4.4 4.5 - - - +
457A ASN 2.8 30.1 + - - +
458A PRO 3.9 0.2 + - - -
460A GLY 3.0 21.4 + - - -
461A VAL 3.7 9.3 + - - +
462A THR* 3.4 12.5 - - + -
463A GLY* 3.0 29.3 + - - +
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Residues in contact with ILE 427 (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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401A ARG* 3.3 4.4 - - - +
402A LEU* 2.8 68.2 + - + +
404A LEU* 5.5 0.4 - - + -
425A GLY 5.8 0.2 - - - +
426A ASN* 1.3 75.6 - - - +
428A ASN* 1.3 74.5 + - + +
429A LEU* 5.5 0.7 - - + -
437A VAL* 4.6 6.3 - - + -
441A MET* 3.4 40.4 - - + -
443A LEU* 5.0 18.2 - - + -
462A THR* 4.3 7.2 - - - -
463A GLY* 4.8 6.3 - - - +
475A LEU* 5.4 1.6 - - + -
477A PHE* 4.6 9.0 - - + -
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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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135A GLU* 5.8 0.6 + - - -
400A ALA 4.1 0.4 - - - -
401A ARG* 3.6 13.0 - - - +
427A ILE* 1.3 90.5 - - + +
429A LEU* 1.3 63.3 + - - +
430A PHE 3.2 20.2 + - - +
431A ASP* 5.3 0.7 - - - -
437A VAL* 3.9 7.6 - - - +
462A THR* 3.5 21.6 + - - +
643A GLN* 2.8 59.9 + - - +
644A TYR* 3.6 10.7 - - - -
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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