Contacts of the helix formed by residues 520 - 533 (chain B) in PDB entry 2NUP
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 GLY 520 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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516B ALA 3.4 1.6 + - - -
517B VAL 3.4 12.5 + - - -
518B GLU 3.2 3.4 - - - -
519B THR* 1.3 81.1 + - - +
521B TYR* 1.3 63.7 + - - +
522B LEU* 3.4 2.9 - - - -
523B ASN* 3.8 25.9 + - - +
524B SER* 4.4 2.9 + - - -
719B TYR* 4.5 1.8 - - - -
721B HIS* 3.9 24.6 - - - +
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Residues in contact with TYR 521 (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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510B PHE* 3.3 16.9 - + + +
511B ASP 3.1 40.8 + - - -
516B ALA* 4.1 7.4 - - + -
519B THR* 3.2 21.7 + - - +
520B GLY* 1.3 73.6 - - - +
522B LEU* 1.3 95.7 + - + +
523B ASN 2.9 4.1 + - - -
524B SER* 3.1 20.4 + - - -
525B VAL* 3.2 24.5 + - + +
637B PHE* 3.5 33.0 + + + -
639B THR* 3.7 23.8 - - + -
692B LEU* 3.7 19.3 - - + -
719B TYR* 3.7 28.0 - - + -
731B LEU* 4.6 1.1 - - + -
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Residues in contact with LEU 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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510B PHE* 4.1 30.7 - - + -
512B VAL* 4.4 20.6 - - + -
516B ALA 6.0 0.9 - - - +
517B VAL* 6.5 1.1 - - - -
520B GLY* 3.4 1.5 - - - -
521B TYR* 1.3 103.9 - - + +
523B ASN* 1.3 68.0 + - - +
525B VAL* 3.5 1.9 + - + +
526B CYS* 3.1 40.0 + - - +
602B LEU* 4.0 13.5 - - + +
603B PRO* 3.8 25.8 - - + +
606B PHE* 4.5 5.2 - - + -
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Residues in contact with ASN 523 (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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520B GLY* 3.8 22.4 - - - +
521B TYR 2.9 1.2 + - - -
522B LEU* 1.3 82.7 - - - +
524B SER* 1.3 63.0 + - - +
526B CYS* 3.2 3.3 + - - +
527B GLN* 2.9 21.2 + - - +
603B PRO* 3.7 34.3 + - + +
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Residues in contact with SER 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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520B GLY 4.4 2.4 + - - -
521B TYR* 3.1 10.2 + - - -
523B ASN* 1.3 79.9 - - - +
525B VAL* 1.3 56.9 + - - +
527B GLN* 3.1 9.0 + - - +
528B SER* 2.7 38.7 + - - -
719B TYR* 3.4 20.9 + - - -
728B VAL* 5.7 6.1 - - - -
731B LEU* 4.5 5.9 - - - +
732B GLN* 3.9 17.2 - - - +
735B LEU* 5.0 1.5 - - - +
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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
----------------------------------------------------------
508B PHE* 5.5 1.1 - - + -
510B PHE* 3.8 22.0 - - + -
521B TYR* 3.3 36.3 - - + +
522B LEU* 3.8 6.5 - - - +
523B ASN 3.2 0.8 - - - -
524B SER* 1.3 77.2 + - - +
526B CYS* 1.3 64.9 + - - +
528B SER* 3.1 3.6 + - - -
529B LEU* 2.9 30.2 + - + +
637B PHE* 3.7 35.7 - - + -
731B LEU* 4.7 6.7 - - + -
735B LEU* 3.9 20.4 - - + -
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Residues in contact with CYS 526 (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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510B PHE* 4.7 5.2 - - - -
522B LEU* 3.1 36.6 + - - +
523B ASN 3.5 8.1 - - - +
525B VAL* 1.3 76.1 - - - +
527B GLN* 1.3 58.1 + - - +
529B LEU* 3.3 4.2 + - - +
530B LEU* 2.9 34.6 + - - +
599B LEU* 3.3 47.5 - - + +
602B LEU* 4.1 8.5 - - - -
603B PRO* 3.8 14.6 - - + -
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Residues in contact with GLN 527 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523B ASN 2.9 13.8 + - - +
524B SER* 3.3 14.8 - - - +
526B CYS* 1.3 76.9 - - - +
528B SER* 1.3 60.2 + - - +
530B LEU* 3.0 24.6 + - - +
531B ASP* 2.7 63.4 + - - +
732B GLN* 5.8 3.6 - - - +
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Residues in contact with SER 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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524B SER 2.7 20.3 + - - -
525B VAL 3.4 4.7 - - - -
527B GLN* 1.3 72.3 - - - +
529B LEU* 1.3 58.4 + - - +
531B ASP* 3.2 8.1 + - - +
532B ASN* 2.7 41.2 + - - +
732B GLN* 3.0 30.6 + - - +
735B LEU* 3.7 25.5 - - - +
736B GLN* 5.7 0.6 - - - -
739B LEU* 4.0 11.4 - - - -
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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
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508B PHE* 3.7 53.8 - - + -
510B PHE* 4.7 7.4 - - + -
525B VAL* 2.9 17.0 + - + +
526B CYS* 3.5 9.0 - - - +
528B SER* 1.3 74.6 - - - +
530B LEU* 1.3 60.4 + - - +
532B ASN* 3.2 0.9 + - - -
533B LEU* 2.8 45.8 + - + +
536B LEU* 4.5 10.8 - - + -
544B ILE* 5.1 0.9 - - + -
546B PHE* 3.9 19.5 - - + -
599B LEU* 3.6 17.5 - - + -
739B LEU* 4.1 19.7 - - + -
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Residues in contact with LEU 530 (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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526B CYS 2.9 19.6 + - - +
527B GLN* 3.4 27.4 - - - +
529B LEU* 1.3 77.5 - - - +
531B ASP* 1.3 64.1 + - - +
532B ASN 3.2 0.3 + - - -
533B LEU* 3.4 15.7 + - + +
596B GLN* 3.4 40.1 + - + +
599B LEU* 3.4 35.4 - - + +
600B LYS* 3.7 30.5 - - + -
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Residues in contact with ASP 531 (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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527B GLN* 2.7 50.9 + - - +
528B SER* 3.5 9.1 + - - +
530B LEU* 1.3 77.7 - - - +
532B ASN* 1.3 67.8 + - - +
533B LEU 3.6 0.2 - - - -
534B ASP* 5.3 1.2 + - - +
535B LEU* 4.9 5.5 - - - +
732B GLN* 5.3 3.3 + - - -
736B GLN* 6.0 0.7 - - - +
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Residues in contact with ASN 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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528B SER* 2.7 33.2 + - - +
529B LEU 3.5 1.8 - - - +
531B ASP* 1.3 84.9 - - - +
533B LEU* 1.3 68.9 + - - +
534B ASP 3.2 2.9 - - - -
535B LEU* 2.9 21.5 + - - +
536B LEU* 3.3 14.5 + - + +
732B GLN* 5.9 0.4 - - - +
736B GLN* 3.3 37.9 + - - +
739B LEU* 3.7 29.4 - - + +
740B THR* 3.8 17.4 - - + +
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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
----------------------------------------------------------
529B LEU* 2.8 33.6 + - + +
530B LEU* 3.4 11.2 + - - +
531B ASP 3.6 0.6 - - - -
532B ASN* 1.3 79.5 - - - +
534B ASP* 1.3 62.8 + - - +
535B LEU 3.2 0.2 + - - -
536B LEU* 3.4 23.3 + - + +
544B ILE* 5.3 4.7 - - + -
546B PHE* 6.0 0.4 - - + -
588B LEU* 3.9 34.8 - - + +
592B LYS* 4.1 17.5 - - + +
595B VAL* 3.8 16.8 - - + -
596B GLN* 3.5 35.2 - - + +
599B LEU* 4.3 16.4 - - + -
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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