Contacts of the helix formed by residues 369 - 373 (chain B) in PDB entry 1F4J
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 369 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367B GLY 3.1 1.0 - - - -
368B PRO* 1.3 77.5 - - - +
370B TYR* 1.3 64.4 + - - +
371B LEU* 3.0 4.0 - - - +
372B HIS* 2.8 49.3 + - + +
389B ASP 3.3 18.7 + - - +
390B GLY* 3.3 11.1 + - - -
391B PRO 2.6 29.2 + - - +
392B MET 3.9 8.5 + - - +
393B CYS* 4.0 2.8 - - - +
63D HIS* 2.9 27.9 + - - -
392D MET* 3.5 11.6 - - + +
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Residues in contact with TYR 370 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B ALA* 3.7 25.1 - - + -
335B ASP* 2.8 29.9 + - - -
359B PRO* 3.6 13.4 - - - +
362B HIS* 3.6 28.7 - - + -
363B ARG* 4.0 20.4 + - + -
366B LEU* 3.6 25.8 - - + -
367B GLY 2.8 25.5 + - - +
368B PRO 4.2 5.8 - - - -
369B ASN* 1.3 70.4 - - - +
371B LEU* 1.3 93.7 + - + +
372B HIS 3.1 0.7 - - - -
373B ILE* 3.1 31.2 + - + +
376B ASN* 3.3 10.3 + - + -
392D MET* 4.3 2.9 - - - -
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Residues in contact with LEU 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B LYS* 6.1 1.1 - - - +
333B ALA 5.8 1.3 - - - +
335B ASP* 4.5 6.5 - - - +
338B ASN* 5.1 3.4 - - - +
369B ASN* 2.9 2.7 + - - -
370B TYR* 1.3 112.7 - - + +
372B HIS* 1.3 64.6 + - + +
373B ILE 3.2 1.8 - - - -
376B ASN* 3.8 21.1 - - + +
377B CYS* 3.2 29.6 - - - +
378B PRO* 4.2 3.0 - - + +
30D GLY* 3.6 39.3 - - - +
31D ALA* 3.9 15.3 - - + +
59D ASP* 4.7 8.5 - - - +
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Residues in contact with HIS 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369B ASN* 2.8 46.4 + - + +
371B LEU* 1.3 82.6 + - + +
373B ILE* 1.3 64.9 + - - +
374B PRO* 3.2 8.0 - - - +
377B CYS* 4.7 7.0 - - - +
383B VAL* 6.6 0.4 - - + -
389B ASP 5.5 0.2 + - - -
392B MET 4.4 0.4 - - - -
393B CYS* 4.5 8.7 - - - -
394B MET* 4.0 26.6 + - + +
395B GLN* 2.8 43.2 + - - +
63D HIS* 5.4 0.9 + - - -
392D MET* 4.8 5.4 - - + -
394D MET* 4.0 7.9 - - + +
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Residues in contact with ILE 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B ALA 4.6 2.0 - - - +
331B GLN* 3.8 44.4 - - + +
366B LEU* 4.4 8.3 - - + -
370B TYR* 3.1 33.8 + - + +
372B HIS* 1.3 76.3 - - - +
374B PRO* 1.3 78.7 - - + +
375B VAL* 4.2 13.7 - - + +
376B ASN* 2.7 33.2 + - - +
377B CYS 3.0 7.8 + - - -
392D MET* 4.0 13.5 - - + +
393D CYS 4.2 2.7 - - - +
394D MET* 4.0 17.3 - - + -
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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
------------------------------------------------------------
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