Contacts of the helix formed by residues 513 - 519 (chain D) in PDB entry 1F6A
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 ARG 513 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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458D ASP* 2.9 48.8 + - + +
512D THR* 1.3 74.7 - - + +
514D ALA* 1.3 66.7 + - - +
515D GLU 2.9 1.4 + - - -
516D TRP* 3.0 50.4 + - + -
517D GLU* 3.3 41.1 + - - +
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Residues in contact with ALA 514 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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512D THR* 3.1 14.3 + - + +
513D ARG* 1.3 79.3 - - - +
515D GLU* 1.3 63.5 + - + +
517D GLU* 3.4 13.3 + - - +
518D GLN* 3.2 20.6 + - - +
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Residues in contact with GLU 515 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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480D HIS* 3.2 39.6 - - + +
485D LEU* 4.8 4.2 - - - +
489D ARG* 2.7 35.2 + - - -
511D VAL* 3.9 9.3 - - + +
512D THR* 2.9 36.4 + - - +
514D ALA* 1.3 79.4 - - + +
516D TRP* 1.3 58.3 + - - +
518D GLN* 3.3 18.8 - - - +
519D LYS 3.1 9.5 - - - +
522D PHE* 4.4 4.5 - - + -
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Residues in contact with TRP 516 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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457D ARG 4.7 4.7 - - - -
458D ASP* 4.3 16.8 - - - -
460D ARG* 4.3 38.1 - - + -
511D VAL* 4.4 8.5 - - + -
512D THR* 3.7 10.3 + - - -
513D ARG* 3.0 58.5 + - + +
515D GLU* 1.3 73.8 - - - +
517D GLU* 1.3 72.4 + - + +
519D LYS 2.7 29.9 - - - +
520D ASP* 3.7 22.0 - - - +
522D PHE* 4.3 14.1 - - + -
543D VAL* 4.7 22.0 - - + -
544D ASN* 4.6 15.7 - - - +
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Residues in contact with GLU 517 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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513D ARG* 3.5 51.3 + - + +
514D ALA* 3.7 12.2 - - - +
515D GLU 3.2 0.6 - - - -
516D TRP* 1.3 89.8 + - + +
518D GLN* 1.3 64.7 + - - +
519D LYS* 3.1 3.3 + - - -
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Residues in contact with GLN 518 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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480D HIS* 4.0 20.5 + - - +
481D ASN* 3.4 29.4 + - - +
483D VAL* 6.1 1.8 - - - +
514D ALA 3.2 12.7 + - - +
515D GLU* 3.3 18.4 - - - +
517D GLU* 1.3 79.7 - - - +
519D LYS* 1.3 62.2 + - + +
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Residues in contact with LYS 519 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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480D HIS* 4.4 13.2 - - + +
481D ASN* 4.0 37.2 - - + +
515D GLU 3.1 3.9 + - - +
516D TRP* 2.7 30.4 - - - +
517D GLU 3.1 2.1 - - - -
518D GLN* 1.3 83.8 - - - +
520D ASP* 1.3 69.1 + - - +
521D GLU* 3.7 40.3 + - + +
522D PHE* 3.8 4.3 - - - -
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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