Contacts of the helix formed by residues 513 - 520 (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 SER 513 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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511B ASP* 3.0 21.5 + - - -
512B VAL* 1.3 80.4 - - - +
514B HIS* 1.3 54.4 + - - +
515B ASN 3.8 2.7 + - - -
516B ALA* 3.1 18.4 + - - +
517B VAL* 2.8 32.4 + - - +
549B PHE 4.1 1.4 + - - -
550B ASP* 4.5 3.4 - - - -
609B THR* 4.8 1.6 - - - -
611B GLU* 3.4 18.6 - - - -
613B GLN 4.3 7.4 - - - -
614B SER* 4.9 0.9 - - - -
639B THR* 3.9 1.0 + - - -
640B GLN* 3.8 23.1 + - - -
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Residues in contact with HIS 514 (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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513B SER* 1.3 67.9 - - - +
515B ASN* 1.3 69.7 + - - +
517B VAL* 3.2 9.8 + - + +
518B GLU* 3.0 28.5 + - + +
609B THR* 4.1 24.6 - - - +
610B LEU* 4.6 10.7 - - + +
611B GLU 2.8 25.5 + - - +
612B THR* 4.4 11.9 + - - -
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Residues in contact with ASN 515 (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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513B SER* 3.4 1.2 + - - -
514B HIS* 1.3 80.9 - - - +
516B ALA* 1.3 63.7 + - - +
518B GLU* 2.9 22.8 + - - +
519B THR* 3.0 24.9 + - - +
612B THR* 5.8 0.6 + - - +
639B THR* 3.4 31.5 + - - +
640B GLN* 3.3 25.4 + - - +
694B GLY* 5.2 6.3 + - - +
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Residues in contact with ALA 516 (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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511B ASP* 3.1 29.6 - - - +
512B VAL* 4.1 0.7 - - - -
513B SER* 3.1 22.3 + - - +
515B ASN* 1.3 79.0 - - - +
517B VAL* 1.3 63.2 + - - +
519B THR* 2.5 26.9 + - - -
520B GLY* 3.4 3.5 + - - -
521B TYR* 4.1 6.8 - - + -
522B LEU* 5.5 1.0 + - - +
639B THR* 3.2 23.2 + - + +
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Residues in contact with VAL 517 (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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512B VAL* 3.5 16.2 - - + +
513B SER 2.8 30.6 + - - +
514B HIS* 3.2 8.7 + - + +
516B ALA* 1.3 72.2 - - - +
518B GLU* 1.3 61.8 + - - +
520B GLY* 3.4 13.0 + - - -
522B LEU* 6.5 0.9 - - - -
606B PHE* 3.5 35.9 - - + +
607B THR* 4.0 22.9 - - + +
609B THR* 4.2 5.2 - - - +
721B HIS* 5.5 1.2 - - - -
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Residues in contact with GLU 518 (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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514B HIS* 3.0 21.0 + - + +
515B ASN* 2.9 20.2 + - - +
517B VAL* 1.3 76.2 - - - +
519B THR* 1.3 61.7 + - + +
520B GLY 3.2 0.4 + - - -
720B HIS* 2.8 33.7 + - + +
721B HIS* 3.7 11.0 - - - -
723B HIS* 5.2 0.5 + - - -
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Residues in contact with THR 519 (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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515B ASN* 3.2 32.5 - - - +
516B ALA* 2.5 19.8 + - - -
518B GLU* 1.3 79.2 - - + +
520B GLY* 1.3 61.4 + - - +
521B TYR* 3.4 20.4 + - - -
639B THR* 4.0 3.2 - - - +
692B LEU 4.4 13.0 - - - +
719B TYR* 3.7 28.7 - - - +
720B HIS* 3.5 7.3 - - + -
721B HIS* 2.9 26.8 + - - -
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Residues in contact with GLY 520 (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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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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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