Contacts of the strand formed by residues 244 - 248 (chain F) in PDB entry 3STJ
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 ILE 244 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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242F LEU* 3.9 22.6 - - + +
243F GLY* 1.3 79.5 - - - +
245F LYS* 1.3 73.3 + - - +
246F GLY* 4.6 0.4 - - - +
265F ALA* 5.8 0.7 - - + -
267F VAL* 3.7 24.7 - - + -
269F GLU 3.6 0.7 - - - -
270F VAL* 3.7 30.1 - - + -
271F LEU* 4.5 4.1 - - - +
276F SER* 3.7 26.5 - - - +
281F VAL* 3.8 9.9 - - + -
287F ILE* 4.5 12.3 - - + -
298F PHE* 4.5 21.0 - - + -
301F LEU* 5.2 1.3 - - + -
316F LEU* 5.7 0.7 - - + -
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Residues in contact with LYS 245 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244F ILE* 1.3 76.9 - - - +
246F GLY* 1.3 59.5 + - - +
267F VAL* 3.8 2.9 - - - +
268F SER* 2.8 30.7 + - - +
269F GLU* 2.8 59.2 + - + +
271F LEU* 4.0 17.7 - - + +
298F PHE* 5.5 0.4 - - - -
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Residues in contact with GLY 246 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244F ILE* 5.2 0.4 - - - -
245F LYS* 1.3 74.9 - - - +
247F THR* 1.3 66.9 + - - +
266F PHE 3.1 14.4 - - - -
267F VAL* 4.4 0.7 - - - -
268F SER* 3.9 7.6 + - - -
298F PHE* 3.7 34.9 - - - -
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Residues in contact with THR 247 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246F GLY* 1.3 77.4 - - - +
248F GLU* 1.3 65.8 + - - +
265F ALA* 3.7 5.0 - - - -
266F PHE* 2.9 47.4 + - - -
268F SER* 5.5 4.7 - - - +
298F PHE* 3.8 9.7 - - - +
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Residues in contact with GLU 248 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247F THR* 1.3 82.3 + - - +
249F MET* 1.3 69.1 + - - +
250F SER* 3.6 5.9 + - - -
253F ILE* 5.0 3.3 - - - +
264F GLY 3.5 5.2 + - - +
266F PHE* 4.5 3.0 - - - +
296F ASN 4.8 0.3 - - - +
297F SER* 3.3 19.2 - - - -
298F PHE* 2.9 37.8 + - + +
299F ALA* 3.1 20.3 + - - +
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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