Contacts of the helix formed by residues 513 - 518 (chain B) in PDB entry 6TXC
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 513 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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360B TYR* 3.0 26.9 + - - -
511B GLU 4.0 1.0 + - - -
512B LYS* 1.3 71.0 - - - +
514B PRO* 1.3 71.7 - - - +
515B ILE* 2.8 24.0 + - - +
516B ASP* 3.2 43.0 + - - +
517B HIS* 3.7 7.8 - - - -
534B LYS* 4.0 9.1 - - - +
545B PHE* 3.4 40.4 - - + -
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Residues in contact with PRO 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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306B ASN* 3.4 25.7 - - + +
363B PHE* 3.6 26.7 - - + -
507B TYR* 3.5 36.6 - - + +
509B MET* 3.9 20.2 - - - -
512B LYS 3.5 9.3 - - - +
513B ASN* 1.3 90.0 - - - +
515B ILE* 1.3 59.2 + - + +
517B HIS* 2.9 28.0 + - - +
518B VAL* 3.6 5.6 - - - +
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Residues in contact with ILE 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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356B VAL* 3.8 17.5 - - + -
359B LEU* 3.6 30.5 - - + -
360B TYR* 3.6 48.0 - - + +
363B PHE* 3.7 24.2 - - + -
513B ASN* 2.8 14.5 + - - +
514B PRO* 1.3 79.3 - - + +
516B ASP* 1.3 60.8 + - - +
518B VAL* 3.2 28.0 + - + +
520B PHE* 3.9 14.6 - - + -
532B ILE 4.2 8.5 + - - +
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Residues in contact with ASP 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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360B TYR* 4.7 0.5 + - - -
513B ASN* 3.2 39.3 + - - +
515B ILE* 1.3 78.4 - - - +
517B HIS* 1.3 65.6 + - + +
518B VAL 3.5 1.1 - - - -
531B ARG* 3.7 19.9 + - - -
532B ILE 4.2 13.8 - - - +
533B THR* 4.2 10.6 - - - -
534B LYS* 4.3 4.9 + - - +
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Residues in contact with HIS 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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305B ARG* 3.5 38.9 + - + +
306B ASN* 3.1 18.6 + - + +
509B MET* 4.0 18.1 - - + +
512B LYS* 4.0 23.4 - - + +
513B ASN 3.7 16.8 - - - -
514B PRO 2.9 14.1 + - - +
516B ASP* 1.3 85.0 + - + +
518B VAL* 1.3 55.9 + - - -
531B ARG* 4.0 11.2 + - - +
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Residues in contact with VAL 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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306B ASN* 3.7 19.7 - - + +
308B ILE* 3.7 22.4 - - + -
334B PHE* 6.3 0.2 - - + -
349B ILE 5.6 2.5 - - - +
351B ALA* 4.7 4.7 - - + +
359B LEU* 4.0 9.6 - - + -
514B PRO 3.6 15.9 - - - +
515B ILE* 3.2 23.1 + - + +
517B HIS* 1.3 79.7 - - - +
519B SER* 1.3 75.6 + - - +
520B PHE* 3.5 34.6 - - + -
531B ARG* 3.7 19.5 + - - -
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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