Contacts of the strand formed by residues 370 - 375 (chain A) in PDB entry 3H8E
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 ALA 370 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261A PRO 3.8 0.6 + - - -
262A PHE* 3.6 12.6 - - + -
263A VAL 2.8 30.2 + - - -
368A PRO* 3.4 3.0 - - - +
369A GLN* 1.4 82.5 - - - +
371A VAL* 1.4 60.7 + - - +
372A ILE* 4.3 4.5 - - + -
399A LEU* 4.1 16.2 - - + -
458A TYR* 5.8 0.4 - - - +
459A ASN* 3.4 9.9 - - + -
490A TYR* 3.3 26.7 - - + +
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Residues in contact with VAL 371 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A VAL* 3.3 14.6 - - + +
265A VAL* 4.0 16.6 - - + -
360A LEU* 3.8 29.6 - - + -
363A ALA* 4.5 3.1 - - + -
368A PRO* 3.3 34.3 - - + -
370A ALA* 1.4 72.8 - - - +
372A ILE* 1.3 64.4 + - - +
373A ASP 4.1 0.2 - - - -
399A LEU* 4.2 0.2 - - - +
458A TYR* 3.4 33.4 - - + +
459A ASN 2.9 6.3 + - - -
460A TRP* 3.1 3.4 - - + -
461A ALA 2.9 23.9 + - - +
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Residues in contact with ILE 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A PHE* 6.3 0.9 - - + -
263A VAL 2.9 7.4 + - - +
264A LEU* 3.4 21.8 - - + -
265A VAL* 2.8 25.6 + - - -
370A ALA* 4.9 2.5 - - + -
371A VAL* 1.3 81.4 - - - +
373A ASP* 1.3 69.8 + - - +
374A ILE* 3.5 10.4 - - + +
399A LEU* 4.3 10.1 - - + -
403A LEU* 3.8 28.0 - - + -
461A ALA* 3.2 10.8 - - + +
463A MET* 3.9 26.5 - - + -
487A LEU* 4.5 2.9 - - + -
490A TYR* 3.7 35.0 - - + +
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Residues in contact with ASP 373 (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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265A VAL* 3.1 25.1 - - + +
356A LEU* 4.3 12.4 - - + +
360A LEU* 4.1 11.6 - - + +
371A VAL 4.1 0.6 - - - -
372A ILE* 1.3 76.4 - - - +
374A ILE* 1.3 64.0 + - - +
451A LEU* 3.2 27.5 - - - +
460A TRP* 3.5 18.0 + - - +
461A ALA 2.9 3.2 + - - +
462A HIS* 2.5 41.8 - - - -
463A MET* 2.9 19.3 + - - +
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Residues in contact with ILE 374 (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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264A LEU* 4.3 6.3 - - + -
265A VAL 2.8 14.3 + - - +
266A GLY* 3.6 0.7 - - - -
267A LYS 3.0 24.1 + - - -
293A GLY* 3.4 8.7 - - - +
296A SER* 3.5 21.1 - - - +
297A VAL* 3.9 15.0 - - + -
356A LEU* 5.0 0.2 - - - +
372A ILE* 3.5 20.4 - - + +
373A ASP* 1.3 78.4 - - - +
375A ALA* 1.3 64.1 + - - +
463A MET* 3.5 18.4 - - + +
465A ILE* 3.5 25.8 - - + -
483A PRO* 3.8 11.4 - - + -
487A LEU* 3.9 31.6 - - + -
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Residues in contact with ALA 375 (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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267A LYS* 3.7 21.8 - - + -
293A GLY* 4.6 2.0 - - - -
356A LEU* 3.7 20.9 - - + -
374A ILE* 1.3 78.8 - - - +
376A THR* 1.3 54.3 + - - +
377A LEU* 3.0 23.0 + - + -
462A HIS* 4.5 4.9 - - + -
463A MET 3.0 9.1 + - - +
464A ASP* 3.2 5.4 - - - -
465A ILE* 2.9 32.1 + - - -
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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