Contacts of the strand formed by residues 244 - 248 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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242D LEU* 3.9 21.3 - - + +
243D GLY* 1.3 75.7 - - - +
245D LYS* 1.3 74.0 + - - +
246D GLY* 5.2 0.4 - - - -
265D ALA* 5.8 0.4 - - + -
267D VAL* 3.7 24.0 - - + -
269D GLU 3.6 0.9 - - - -
270D VAL* 3.7 30.1 - - + -
271D LEU* 5.1 3.4 - - - +
276D SER* 3.4 31.0 - - - +
281D VAL* 3.8 11.7 - - + -
287D ILE* 4.5 12.1 - - + -
298D PHE* 4.5 21.0 - - + -
301D LEU* 5.2 0.7 - - + -
316D LEU* 5.7 0.4 - - + -
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Residues in contact with LYS 245 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244D ILE* 1.3 79.5 - - - +
246D GLY* 1.3 58.9 + - - +
267D VAL* 3.8 2.9 - - - -
268D SER* 2.9 31.2 + - - +
269D GLU* 2.8 58.4 + - + +
271D LEU* 4.1 17.0 - - + -
298D PHE* 5.4 0.7 - - - -
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Residues in contact with GLY 246 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244D ILE* 5.2 0.7 - - - -
245D LYS* 1.3 75.3 - - - +
247D THR* 1.3 66.2 - - - +
266D PHE 3.1 14.1 - - - -
267D VAL* 4.4 1.1 - - - -
268D SER* 3.9 8.2 + - - -
298D PHE* 3.7 34.4 - - - -
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Residues in contact with THR 247 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246D GLY* 1.3 77.7 - - - +
248D GLU* 1.3 65.2 + - - +
265D ALA* 3.7 5.0 - - - -
266D PHE* 2.9 47.7 + - - -
268D SER* 5.7 4.7 - - - +
298D PHE* 3.8 10.8 - - - +
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Residues in contact with GLU 248 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247D THR* 1.3 82.4 + - - +
249D MET* 1.3 70.5 + - - +
250D SER* 3.6 6.2 + - - -
253D ILE* 5.0 3.5 - - - +
264D GLY 3.4 5.5 + - - +
266D PHE* 4.4 2.2 - - - +
297D SER* 3.3 19.7 - - - -
298D PHE* 2.9 38.3 + - + +
299D ALA* 3.1 19.8 + - - +
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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