Contacts of the helix formed by residues 521 - 536 (chain B) in PDB entry 5UFL
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 ASN 521 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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519B SER* 3.0 12.7 + - - +
520B ASP* 1.3 82.5 + - - +
522B ARG* 1.3 63.8 + - - +
523B GLU* 2.8 40.8 + - - +
524B GLN* 3.0 22.0 + - + +
525B VAL* 3.2 24.9 + - - +
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Residues in contact with ARG 522 (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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547A GLY 5.0 0.6 - - - +
548A GLU* 4.2 27.1 - - + +
551A ALA* 3.9 19.7 - - + -
520B ASP 3.4 4.4 + - - -
521B ASN* 1.3 72.4 + - - +
523B GLU* 1.3 98.0 + - - +
525B VAL* 3.4 2.4 + - - +
526B GLN* 3.1 44.5 + - + +
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Residues in contact with GLU 523 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521B ASN* 2.8 20.5 + - - +
522B ARG* 1.3 112.3 + - - +
524B GLN* 1.3 55.6 + - - +
526B GLN* 3.3 9.3 + - - +
527B SER* 2.9 29.2 + - - -
530B ARG* 5.2 0.5 + - - -
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Residues in contact with GLN 524 (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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473B LYS 5.4 2.2 + - - -
477B ASP* 3.6 29.8 + - - +
480B LEU* 6.2 0.4 - - - +
481B LYS* 6.0 0.9 - - - +
515B PHE* 4.6 5.2 + - - +
516B ALA* 3.7 26.9 - - - +
519B SER* 2.7 33.6 + - - +
521B ASN* 3.0 26.8 + - + +
523B GLU* 1.3 76.7 - - - +
525B VAL* 1.3 57.8 + - - +
527B SER* 3.2 8.7 + - - -
528B GLY 2.9 25.6 + - - -
557B ARG* 5.3 2.6 + - - +
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Residues in contact with VAL 525 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547A GLY* 3.5 29.8 - - - +
550A ILE* 3.8 23.3 - - + -
551A ALA* 4.0 10.3 - - + -
554A ASN* 4.3 0.4 - - - +
516B ALA 3.4 17.5 - - - +
517B LEU* 4.0 13.6 - - + +
519B SER 3.2 27.6 - - - +
521B ASN 3.2 13.9 + - - +
522B ARG 3.8 4.0 - - - +
524B GLN* 1.3 78.7 - - - +
526B GLN* 1.3 58.4 + - - +
528B GLY* 3.8 0.3 - - - -
529B LEU* 2.9 33.3 + - + +
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Residues in contact with GLN 526 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543A ALA 4.0 8.0 - - - +
544A LEU* 3.1 50.5 + - + +
547A GLY* 3.9 18.5 - - - -
548A GLU* 4.0 11.1 + - - +
522B ARG* 3.1 29.6 + - + +
523B GLU* 3.6 11.4 - - - +
525B VAL* 1.3 74.3 - - - +
527B SER* 1.3 59.3 + - - +
529B LEU* 4.0 5.6 - - - +
530B ARG* 3.1 43.4 + - - +
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Residues in contact with SER 527 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480B LEU* 4.4 24.9 + - - +
481B LYS* 5.1 3.6 + - - +
484B ASP* 4.7 10.9 + - - +
523B GLU 2.9 13.6 + - - -
524B GLN* 3.4 11.2 - - - -
526B GLN* 1.3 76.8 - - - +
528B GLY* 1.3 62.0 + - - +
530B ARG* 3.4 20.4 + - - +
531B ILE* 3.2 25.6 + - - +
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Residues in contact with GLY 528 (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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480B LEU* 3.8 22.2 - - - +
513B LEU* 3.4 11.3 - - - +
516B ALA* 3.9 9.3 - - - +
517B LEU* 3.9 7.0 - - - -
524B GLN 2.9 14.3 + - - -
525B VAL 3.9 0.7 - - - -
527B SER* 1.3 73.8 - - - +
529B LEU* 1.3 60.0 + - - +
531B ILE* 3.4 1.0 + - - -
532B LEU* 2.8 29.5 + - - +
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Residues in contact with LEU 529 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532A LEU* 4.2 18.6 - - + -
543A ALA* 3.4 29.6 - - + +
546A LEU* 4.2 16.2 - - + -
547A GLY* 3.8 22.2 - - - +
550A ILE* 4.6 6.3 - - + -
517B LEU* 3.6 13.9 - - + +
525B VAL* 2.9 19.3 + - + +
526B GLN* 4.0 7.2 - - - +
528B GLY* 1.3 75.2 - - - +
530B ARG* 1.3 60.6 + - - +
532B LEU* 4.1 8.7 - - + -
533B LEU* 3.2 54.5 + - + +
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Residues in contact with ARG 530 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484B ASP* 2.9 37.9 + - - +
487B ASN* 4.5 18.9 + - - +
488B LYS* 4.7 6.2 - - - +
523B GLU 5.2 0.6 + - - -
526B GLN* 3.1 40.7 + - - +
527B SER* 3.5 15.2 + - - +
528B GLY 3.2 0.2 - - - -
529B LEU* 1.3 77.0 - - - +
531B ILE* 1.3 64.5 + - + +
533B LEU* 3.7 5.7 + - - +
534B GLU* 3.5 22.9 + - - +
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Residues in contact with ILE 531 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480B LEU* 4.5 14.6 - - + +
483B LEU* 3.8 44.6 - - + +
484B ASP* 4.0 9.0 - - + +
487B ASN* 5.0 6.7 - - + +
500B PHE* 4.5 13.2 - - + -
504B LEU* 4.3 8.9 - - + +
509B LEU* 4.3 20.2 - - + -
513B LEU* 4.0 16.4 - - + -
527B SER* 3.2 16.7 + - - +
528B GLY* 3.4 6.5 + - - +
530B ARG* 1.3 75.7 - - + +
532B LEU* 1.3 65.4 + - - +
534B GLU* 3.3 6.7 + - + +
535B ALA* 3.0 20.7 + - + +
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Residues in contact with LEU 532 (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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529A LEU* 4.0 18.6 - - + -
532A LEU* 4.1 18.4 - - + -
533A LEU* 4.2 14.4 - - + -
513B LEU* 4.0 10.7 - - + +
517B LEU* 3.6 24.5 - - + -
528B GLY 2.8 21.9 + - - +
529B LEU* 3.7 12.6 - - + +
531B ILE* 1.3 72.7 - - - +
533B LEU* 1.3 59.2 + - + +
535B ALA* 3.1 4.9 + - - -
536B ALA* 2.8 31.4 + - - +
541B PHE* 3.8 19.1 - - + -
546B LEU* 3.4 26.7 - - + -
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Residues in contact with LEU 533 (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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532A LEU* 4.4 15.3 - - + -
533A LEU* 4.9 4.0 - - + -
536A ALA* 3.5 37.8 - - + +
541A PHE* 5.0 5.2 - - + -
543A ALA* 4.0 26.9 - - + -
529B LEU* 3.2 35.3 + - + +
530B ARG* 4.2 5.6 - - - +
532B LEU* 1.3 84.5 - - + +
534B GLU* 1.3 56.9 + - - +
536B ALA* 4.1 4.2 - - - +
537B PRO* 3.2 22.2 - - - +
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Residues in contact with GLU 534 (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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487B ASN* 3.9 16.3 + - - +
490B LYS* 3.6 13.5 + - - -
500B PHE* 3.7 25.1 - - + -
501B TYR* 3.3 24.4 + - + -
504B LEU* 3.8 7.2 - - + +
530B ARG* 3.5 13.7 + - - +
531B ILE* 3.3 11.2 + - - +
532B LEU 3.2 0.2 - - - -
533B LEU* 1.3 79.9 - - - +
535B ALA* 1.3 57.4 + - - +
537B PRO* 3.6 6.9 - - - +
538B LEU* 3.2 21.5 - - - +
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Residues in contact with ALA 535 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504B LEU* 3.7 30.9 - - + +
509B LEU* 5.3 2.0 - - + -
513B LEU* 5.3 1.6 - - + -
531B ILE* 3.0 18.7 + - + +
532B LEU* 3.7 4.3 - - - +
534B GLU* 1.3 77.3 - - - +
536B ALA* 1.3 63.6 + - - +
537B PRO* 3.5 0.4 - - - -
538B LEU* 3.4 21.2 + - - +
541B PHE* 3.6 33.6 - - + -
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Residues in contact with ALA 536 (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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533A LEU* 3.3 49.4 - - + +
536A ALA* 6.1 1.1 - - + -
532B LEU* 2.8 18.0 + - + +
533B LEU* 4.2 5.4 - - + +
535B ALA* 1.3 74.4 - - - +
537B PRO* 1.4 68.4 - - + +
538B LEU 3.2 7.2 + - - +
541B PHE* 4.1 18.1 - - - +
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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