Contacts of the helix formed by residues 381 - 387 (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 ASP 381 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A TYR* 2.6 37.5 + - - +
152A TYR* 4.0 9.1 + - - -
380A THR* 1.3 74.6 - - - +
382A PRO* 1.4 67.1 - - - +
383A VAL* 3.2 20.1 + - - +
384A SER* 3.0 29.8 + - - +
385A GLN* 2.8 30.8 + - - +
422A LEU* 3.6 11.0 - - + +
431A LEU* 3.7 16.9 - - + +
438A GLY 4.9 1.6 + - - -
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Residues in contact with PRO 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A TYR* 3.8 8.3 - - + +
156A PHE* 3.7 25.8 - - + -
380A THR 3.4 9.9 - - - +
381A ASP* 1.4 91.1 - - - +
383A VAL* 1.3 56.4 + - + +
385A GLN* 3.2 12.0 + - + +
386A LYS* 2.9 35.3 + - + +
419A SER* 3.4 23.3 - - - +
420A GLN 3.4 21.1 - - - +
421A PRO 4.1 1.3 - - - +
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Residues in contact with VAL 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A TYR* 4.7 3.6 - - + -
152A TYR* 3.4 66.6 - - + +
153A GLY* 4.3 8.3 - - - -
155A GLU* 5.4 1.6 - - - +
156A PHE* 5.6 1.1 - - + -
381A ASP* 3.2 16.1 + - - +
382A PRO* 1.3 79.6 - - + +
384A SER* 1.3 64.4 + - - +
386A LYS* 3.2 28.5 + - + +
387A ASN* 3.5 4.3 + - - +
435A ASN* 4.9 7.3 + - - +
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Residues in contact with SER 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A TYR* 5.2 0.9 + - - -
381A ASP* 3.0 31.1 + - - +
383A VAL* 1.3 78.0 - - - +
385A GLN* 1.3 68.0 + - - +
387A ASN* 2.9 26.7 + - - +
390A VAL* 3.3 27.4 - - - +
394A VAL* 5.1 1.3 - - - -
431A LEU* 4.8 1.2 - - - +
435A ASN* 3.5 29.3 + - - +
436A ILE 3.9 6.5 + - - -
438A GLY 6.1 0.2 - - - -
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Residues in contact with GLN 385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A THR* 4.3 14.1 + - - +
381A ASP 2.8 23.8 + - - +
382A PRO* 3.2 11.0 + - + +
384A SER* 1.3 86.0 - - - +
386A LYS* 1.3 58.0 + - - +
387A ASN 2.8 18.0 - - - +
388A GLU* 4.1 1.6 + - - +
391A ARG* 3.0 46.3 + - + +
394A VAL* 3.3 40.6 - - - +
395A GLU* 4.8 7.9 + - - -
398A LEU* 5.3 0.6 - - - +
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Residues in contact with LYS 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382A PRO* 2.9 19.5 + - + +
383A VAL* 3.2 21.5 + - + +
385A GLN* 1.3 75.2 - - + +
387A ASN* 1.3 56.4 + - - +
388A GLU* 3.7 14.4 + - - +
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Residues in contact with ASN 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A VAL 3.5 3.9 + - - +
384A SER 2.9 20.6 + - - +
385A GLN 2.8 13.4 - - - +
386A LYS* 1.3 75.3 - - - +
388A GLU* 1.3 67.9 + - - +
389A SER* 3.7 4.6 + - - -
390A VAL* 3.6 22.7 - - + +
391A ARG 2.9 14.4 + - - -
435A ASN* 5.1 15.3 + - - +
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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