Contacts of the helix formed by residues 531 - 537 (chain A) in PDB entry 5FN3
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 531 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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477A LEU* 4.3 15.0 - - + +
523A TYR* 3.4 18.4 - - - -
524A GLY* 3.5 19.2 - - - +
528A LYS* 2.4 55.1 + - - +
529A ALA 2.7 18.2 + - - +
530A ASN* 1.3 73.9 - - - +
532A SER* 1.3 69.0 + - - +
533A TRP 3.3 4.3 - - - +
534A PHE* 4.2 8.5 - - + +
535A GLN* 2.9 28.8 + - - +
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Residues in contact with SER 532 (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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474A GLU* 4.7 8.4 - - - +
477A LEU* 3.1 21.9 - - - +
531A ASN* 1.3 74.5 - - - +
533A TRP* 1.3 72.5 + - - +
535A GLN* 3.8 6.5 - - - +
536A SER* 3.0 24.1 + - - -
608A PRO* 5.5 1.4 - - - +
609A LEU* 6.3 4.7 - - - -
616A ARG* 4.9 3.0 + - - +
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Residues in contact with TRP 533 (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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477A LEU* 4.5 7.4 - - + -
517A THR* 5.1 7.4 - - + -
520A ARG* 3.5 58.9 - - + +
521A LEU* 3.9 31.4 - - + -
531A ASN* 3.3 1.4 - - - +
532A SER* 1.3 83.5 + - - +
534A PHE* 1.3 84.6 + + + +
536A SER* 2.3 32.4 + - - -
537A ILE* 3.0 25.2 - - + +
570A ALA* 5.1 3.1 - - + -
573A ASN* 3.9 24.3 - - + +
574A LEU* 3.6 31.9 - - + -
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Residues in contact with PHE 534 (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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477A LEU* 6.3 1.1 - - + -
520A ARG 5.1 0.4 - - - -
521A LEU* 4.5 7.0 - - + -
524A GLY* 3.2 41.1 - - - -
525A PHE* 3.4 37.5 - + - -
529A ALA* 3.4 28.5 - - - +
531A ASN* 3.4 7.4 + - + +
532A SER 3.4 0.2 - - - -
533A TRP* 1.3 106.8 - + + +
535A GLN* 1.3 61.7 + - - +
537A ILE* 3.0 30.2 + - + +
538A LEU* 3.7 6.1 - - - +
546A LEU* 3.8 16.6 - - + +
551A LEU* 4.8 1.8 - - + -
566A VAL* 3.3 30.2 - - + +
570A ALA* 5.1 2.0 - - + -
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Residues in contact with GLN 535 (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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530A ASN* 2.9 31.7 + - - +
531A ASN 2.9 21.3 + - - +
532A SER* 3.8 5.6 - - - +
534A PHE* 1.3 78.1 - - - +
536A SER* 1.3 62.5 + - - +
537A ILE 3.1 1.4 + - - -
538A LEU* 3.4 18.0 + - + +
543A ARG* 4.7 30.2 + - + +
546A LEU* 3.7 16.1 - - + +
606A GLN* 3.5 19.3 + - - +
609A LEU* 5.5 2.4 - - - +
616A ARG* 2.9 34.7 + - - +
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Residues in contact with SER 536 (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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532A SER 3.0 13.1 + - - -
533A TRP* 2.3 40.7 + - - -
535A GLN* 1.3 77.7 - - - +
537A ILE* 1.3 57.9 + - - +
538A LEU 3.7 0.2 - - - -
573A ASN* 5.4 0.9 - - - +
605A VAL* 3.5 3.3 - - - +
606A GLN 2.9 23.7 - - - +
607A GLY* 3.6 29.5 + - - -
608A PRO* 4.0 12.8 - - - -
616A ARG* 4.5 0.2 - - - +
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Residues in contact with ILE 537 (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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533A TRP* 3.0 47.3 - - + +
534A PHE* 3.0 25.3 + - + +
536A SER* 1.3 79.6 - - - +
538A LEU* 1.3 71.7 + - - +
566A VAL* 5.1 3.2 - - + +
569A TYR* 2.9 48.7 - - + +
570A ALA* 4.5 11.9 - - - +
572A ALA* 5.1 1.6 - - + -
573A ASN* 3.7 33.4 - - + +
605A VAL* 3.8 10.8 - - + -
621A VAL* 5.9 2.7 - - + -
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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