Contacts of the strand formed by residues 378 - 381 (chain A) in PDB entry 4S15
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 THR 378 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299A THR 5.1 0.5 + - - -
302A THR* 5.2 8.4 - - + +
372A PHE* 3.4 10.7 - - - -
373A ASP* 2.8 51.0 + - - +
376A ASN* 3.6 16.8 - - + +
377A ASN* 1.3 82.4 - - - +
379A VAL* 1.3 61.5 + - - +
385A TYR* 3.4 23.4 - - + +
386A ALA 3.1 15.3 - - - +
387A SER* 3.8 18.8 - - - +
404A PHE* 4.0 0.7 - - - -
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Residues in contact with VAL 379 (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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368A MET* 3.7 21.8 - - + -
371A ALA 3.5 11.0 - - - +
372A PHE* 3.8 12.3 - - + -
378A THR* 1.3 75.4 - - - +
380A TYR* 1.3 64.1 + - - +
381A PHE* 3.3 3.9 + - + -
385A TYR* 3.7 4.7 - - - -
386A ALA* 2.7 37.3 + - - +
391A PHE* 4.4 15.5 - - + -
404A PHE* 3.6 25.4 - - + -
601A 4D8 3.6 36.1 - - + -
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Residues in contact with TYR 380 (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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290A TYR* 3.9 39.2 + + - -
295A LEU* 3.7 19.7 - - + -
298A ILE* 3.9 24.3 - - + +
301A GLN* 4.5 1.6 + - - -
371A ALA* 2.9 27.6 + - + +
379A VAL* 1.3 69.9 - - - +
381A PHE* 1.3 59.8 + - - +
382A ASP 5.8 0.2 - - - -
383A GLY* 3.5 41.6 + - - -
384A LYS* 3.5 12.3 - - - -
385A TYR* 3.6 29.3 - + + +
601A 4D8 3.6 31.4 - - + +
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Residues in contact with PHE 381 (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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303A PHE* 3.1 19.7 - + - -
311A TYR* 4.1 12.8 - + - -
319A MET* 4.1 6.3 - - + -
322A LEU* 4.1 21.1 - - + -
323A CYS* 4.2 7.6 - - - -
326A LYS* 4.0 14.1 - - + -
379A VAL* 3.3 11.4 + - + +
380A TYR* 1.3 76.4 - - - +
382A ASP* 1.3 81.7 + - + +
383A GLY 3.1 0.9 - - - -
384A LYS 2.8 18.4 + - - +
386A ALA* 4.2 6.7 - - + -
390A VAL* 4.1 23.1 - - + -
391A PHE* 3.9 30.5 - + + -
601A 4D8 3.9 38.1 - - + -
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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
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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