Contacts of the helix formed by residues 373 - 378 (chain B) in PDB entry 3AFF
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 PRO 373 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379A ILE* 6.3 0.4 - - + -
380A PHE* 4.0 16.2 - - + -
384A GLU* 3.5 24.2 - - + +
120B TYR 5.7 0.4 - - - +
121B ALA* 4.3 16.4 - - + -
122B PRO* 4.0 13.5 - - + -
371B ASN 3.3 9.6 - - - +
372B ASP* 1.4 88.8 - - - +
374B GLU* 1.3 57.6 + - + +
375B ARG 3.1 0.2 - - - -
376B ALA* 2.8 23.0 + - + +
377B TYR* 3.2 35.4 + - + +
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Residues in contact with GLU 374 (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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120B TYR* 6.0 0.3 - - - +
210B TYR* 4.1 7.3 + - - -
233B TRP* 2.7 31.5 + - - -
237B HIS* 3.2 27.3 + - - +
323B ARG* 3.2 31.9 + - - +
372B ASP* 3.2 19.7 + - - +
373B PRO* 1.3 72.5 - - + +
375B ARG* 1.3 66.9 + - - +
376B ALA 3.0 2.9 + - - -
377B TYR* 3.1 30.7 + - + +
378B VAL* 3.4 18.3 + - + +
393B MET* 3.5 13.5 - - + +
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Residues in contact with ARG 375 (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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379A ILE* 3.6 41.1 + - + +
323B ARG* 5.5 4.8 - - - +
366B ARG* 5.5 7.3 - - - +
369B ALA 4.1 10.5 - - - +
370B ALA* 3.0 34.7 + - - +
371B ASN* 5.2 0.8 - - - +
372B ASP* 3.2 24.0 + - + +
374B GLU* 1.3 78.3 - - - +
376B ALA* 1.3 58.0 + - - +
378B VAL* 3.7 17.3 - - - +
379B ILE* 4.0 9.5 - - - +
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Residues in contact with ALA 376 (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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376A ALA* 3.6 31.3 - - + +
379A ILE* 3.9 14.6 - - + -
380A PHE* 3.5 27.8 - - + -
373B PRO* 2.8 14.9 + - + +
375B ARG* 1.3 73.9 - - - +
377B TYR* 1.3 68.2 + - - +
378B VAL 3.1 2.5 - - - -
379B ILE* 2.9 21.2 + - - +
380B PHE* 3.7 1.8 + - - -
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Residues in contact with TYR 377 (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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380A PHE* 4.0 18.8 - + - -
385A PHE* 4.2 5.4 - + - -
120B TYR 4.9 2.3 + - - -
122B PRO* 3.3 32.7 - - - +
166B PHE* 3.6 14.0 - + - -
210B TYR* 4.4 12.3 - + - -
373B PRO* 3.4 20.0 - - + +
374B GLU* 3.1 32.3 + - + +
376B ALA* 1.3 76.2 - - - +
378B VAL* 1.3 58.1 + - - +
379B ILE 3.0 6.2 + - - -
380B PHE* 3.0 28.2 + + - +
387B LEU* 3.5 42.9 - - + +
388B PRO 5.2 0.5 - - - +
390B GLY* 3.4 11.5 - - - -
393B MET* 4.2 21.7 - - + +
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Residues in contact with VAL 378 (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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323B ARG* 4.5 11.0 - - - +
374B GLU 3.4 11.8 + - - +
375B ARG* 3.7 17.0 - - - +
377B TYR* 1.3 78.2 - - - +
379B ILE* 1.3 64.3 + - + +
380B PHE 3.5 0.4 - - - +
390B GLY* 3.4 27.3 - - - +
391B ASP* 4.0 8.0 + - - +
393B MET* 3.8 10.5 - - + +
394B VAL* 3.4 42.6 - - + +
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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