Contacts of the strand formed by residues 363 - 367 (chain A) in PDB entry 4A3I
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 GLN 363 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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358A ASN 4.9 1.0 - - - +
359A LEU* 3.9 26.1 - - + +
360A GLU* 2.9 47.2 + - - +
361A LEU 3.7 5.9 - - - +
362A ASP* 1.3 75.6 - - - +
364A VAL* 1.4 58.9 + - - +
439A ASN* 4.4 4.0 + - - -
458A HIS* 3.0 17.0 + - - -
459A ARG* 3.3 40.3 + - + +
460A VAL 4.2 4.9 + - - -
461A LYS* 3.5 27.0 + - + +
469A ARG 4.4 3.5 - - - +
470A LEU* 4.6 6.8 - - - -
471A ASN 4.6 1.4 + - - -
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Residues in contact with VAL 364 (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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359A LEU* 4.4 2.0 - - - -
363A GLN* 1.4 74.4 - - - +
365A GLY* 1.3 71.6 + - - +
366A VAL* 3.4 14.1 + - + +
442A VAL* 3.9 18.4 - - + -
444A PHE* 3.8 36.6 - - + -
458A HIS* 3.5 27.4 - - + +
459A ARG 2.8 13.3 + - - +
461A LYS* 3.1 24.2 + - - -
468A PHE* 4.6 4.0 - - + -
469A ARG 3.5 11.4 - - - +
470A LEU* 4.8 0.7 - - + -
489A LEU* 4.4 7.4 - - + -
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Residues in contact with GLY 365 (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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359A LEU* 3.7 12.6 - - - +
364A VAL* 1.3 68.9 - - - +
366A VAL* 1.3 60.9 + - - -
461A LYS* 3.3 9.2 - - - -
463A ILE* 3.5 18.4 - - - -
467A THR 3.9 0.2 - - - +
468A PHE* 3.1 16.6 - - - +
469A ARG* 2.7 38.2 + - - -
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Residues in contact with VAL 366 (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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364A VAL* 3.5 28.9 - - + +
365A GLY* 1.3 74.2 - - - +
367A PRO* 1.4 80.4 - - + +
370A ILE* 3.8 23.6 - - + -
371A ALA* 4.0 12.6 - - + +
374A LEU* 5.2 0.4 - - + -
436A ILE* 5.0 4.0 - - + -
460A VAL* 3.8 25.4 - - + -
461A LYS 2.9 6.3 + - - -
462A VAL* 3.4 6.5 - - + +
463A ILE* 3.0 20.4 + - - +
468A PHE* 4.2 6.3 - - + -
489A LEU* 4.4 17.5 - - + -
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Residues in contact with PRO 367 (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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366A VAL* 1.4 85.1 - - + +
368A LYS* 1.4 55.1 + - - +
369A SER* 4.5 8.7 - - - +
370A ILE* 3.1 25.5 + - + +
371A ALA* 2.8 31.4 + - - +
463A ILE* 3.2 9.4 - - + +
465A TYR 3.5 13.2 - - - +
466A SER* 3.5 30.1 - - - +
467A THR 3.5 15.7 - - - +
468A PHE* 3.7 21.3 - - + -
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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