Contacts of the helix formed by residues 508 - 516 (chain A) 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 THR 508 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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505A ASP* 2.6 24.3 + - - +
507A GLN* 1.3 81.1 + - - +
509A GLN* 1.3 61.2 + - - +
510A ILE 3.4 2.1 + - - -
511A GLN* 3.5 32.7 + - + +
512A ASN* 2.5 52.4 + - - +
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Residues in contact with GLN 509 (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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25A PRO* 4.4 0.5 - - - +
26A SER* 3.6 24.2 + - - +
27A SER* 2.9 31.2 + - - -
30A GLU* 3.5 36.0 + - - +
504A ALA* 3.9 11.9 - - + +
505A ASP 2.8 13.5 + - - +
506A ALA* 3.7 23.2 + - - +
507A GLN 3.8 0.2 - - - -
508A THR* 1.3 77.7 - - - +
510A ILE* 1.3 60.1 + - + +
512A ASN* 4.3 0.2 - - - +
513A ILE* 3.0 29.5 + - - +
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Residues in contact with ILE 510 (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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30A GLU* 3.2 35.2 - - + +
508A THR 3.6 0.2 - - - -
509A GLN* 1.3 73.3 - - + +
511A GLN* 1.3 60.1 + - + +
512A ASN 3.2 2.5 - - - -
513A ILE* 4.2 7.0 - - + -
514A ALA* 2.7 33.8 + - + +
556A LYS* 3.4 32.8 - - + +
557A PHE* 3.6 30.1 - - + -
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Residues in contact with GLN 511 (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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507A GLN 4.2 5.5 + - - -
508A THR* 3.5 38.3 + - + +
510A ILE* 1.3 79.7 - - + +
512A ASN* 1.3 61.8 + - - +
514A ALA* 3.6 5.7 + - - +
515A ALA* 3.1 20.8 + - - +
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Residues in contact with ASN 512 (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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23A VAL* 4.0 22.2 - - + +
504A ALA* 5.2 0.4 - - + -
505A ASP* 3.9 24.1 + - - +
508A THR* 2.5 49.6 + - - +
509A GLN* 4.3 2.2 - - - +
510A ILE 3.2 0.2 - - - -
511A GLN* 1.3 76.8 - - - +
513A ILE* 1.3 60.7 + - - +
515A ALA* 2.8 23.5 + - - +
516A SER* 2.9 15.8 + - - -
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Residues in contact with ILE 513 (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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21A TRP* 3.0 49.2 - - + -
23A VAL* 4.3 23.1 - - + +
24A TRP 4.8 0.4 - - - -
25A PRO* 4.4 18.2 - - + -
30A GLU* 4.1 22.9 - - + -
34A MET* 4.4 17.3 - - + -
504A ALA* 4.4 3.6 - - + -
509A GLN* 3.0 27.1 - - - +
510A ILE* 3.6 11.4 - - + +
512A ASN* 1.3 76.5 - - - +
514A ALA* 1.3 63.4 + - - +
516A SER* 3.0 16.5 + - - -
517A PHE 3.5 0.2 + - - -
557A PHE* 4.7 6.3 - - + -
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Residues in contact with ALA 514 (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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510A ILE* 2.7 22.1 + - + +
511A GLN* 3.7 7.4 - - - +
513A ILE* 1.3 74.7 - - - +
515A ALA* 1.3 60.6 + - - +
517A PHE 3.5 2.3 + - - -
557A PHE* 3.6 30.2 - - + -
573A THR* 3.3 8.7 - - - +
574A PHE* 3.2 29.1 - - + -
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Residues in contact with ALA 515 (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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4A TYR* 4.0 47.1 - - + +
511A GLN 3.1 13.8 + - - +
512A ASN* 2.8 12.4 + - - +
514A ALA* 1.3 78.8 - - - +
516A SER* 1.3 56.9 + - - +
517A PHE 3.2 5.0 + - - +
573A THR* 4.1 14.3 + - - +
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Residues in contact with SER 516 (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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4A TYR* 4.9 11.4 - - - -
21A TRP* 3.6 3.4 - - - -
22A ASN* 3.1 36.8 + - - +
23A VAL* 3.1 53.9 + - - +
512A ASN 2.9 5.3 + - - -
513A ILE* 3.0 14.3 + - - -
515A ALA* 1.3 74.6 - - - +
517A PHE* 1.3 62.1 + - - +
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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