Contacts of the strand formed by residues 265 - 270 (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 ALA 265 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244D ILE* 5.8 0.2 - - + -
247D THR 3.7 4.3 - - - -
249D MET* 4.1 3.1 - - - +
264D GLY* 1.3 71.7 - - - -
266D PHE* 1.3 61.4 + - - +
267D VAL* 3.8 1.7 + - + -
285D ASP 3.6 0.5 - - - +
286D ILE* 3.2 7.0 - - - +
287D ILE* 2.8 55.1 + - + +
295D LEU* 5.3 0.4 - - - +
298D PHE* 3.3 34.5 - - + -
301D LEU* 4.4 10.8 - - + -
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Residues in contact with PHE 266 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246D GLY* 3.1 6.5 - - - -
247D THR* 2.9 51.8 + - - +
248D GLU 4.4 4.5 - - - +
249D MET* 3.6 30.4 - - + +
253D ILE* 4.2 25.6 - - + -
257D PHE* 5.0 9.0 - + - -
265D ALA* 1.3 72.3 - - - +
267D VAL* 1.3 68.5 + - - +
268D SER* 3.6 10.4 + - - -
284D GLY* 4.0 27.4 - - - -
285D ASP 3.7 1.8 - - - -
286D ILE* 3.9 10.3 - - + -
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Residues in contact with VAL 267 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244D ILE* 3.7 32.8 - - + -
245D LYS 3.8 4.9 - - - +
246D GLY* 4.4 0.7 - - - -
265D ALA* 4.5 1.8 - - + +
266D PHE* 1.3 75.7 - - - +
268D SER* 1.3 59.1 + - - +
269D GLU 3.8 13.2 - - - +
270D VAL* 3.8 12.8 - - + -
281D VAL* 4.5 2.5 - - + -
282D LYS 4.1 11.7 - - - +
283D ALA* 4.2 0.9 - - - -
284D GLY* 2.6 30.8 + - - -
285D ASP* 2.9 28.5 + - + +
287D ILE* 3.8 33.4 - - + -
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Residues in contact with SER 268 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245D LYS* 2.9 24.1 + - - +
246D GLY* 3.9 6.5 - - - -
247D THR* 5.5 3.9 - - - +
266D PHE* 3.6 13.1 + - - -
267D VAL* 1.3 73.9 - - - +
269D GLU* 1.3 64.2 + - - +
283D ALA* 3.4 16.9 - - - +
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Residues in contact with GLU 269 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244D ILE* 3.6 3.3 - - - -
245D LYS* 2.8 72.4 + - + +
267D VAL* 3.7 3.3 - - - +
268D SER* 1.3 83.1 - - - +
270D VAL* 1.3 71.2 + - - +
271D LEU* 3.5 21.4 + - + +
272D PRO* 5.9 1.0 - - - +
283D ALA* 4.5 3.6 - - - -
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Residues in contact with VAL 270 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243D GLY 3.6 3.4 - - - +
244D ILE* 3.7 14.4 - - + -
267D VAL* 3.8 2.9 - - + -
269D GLU* 1.3 80.9 - - - +
271D LEU* 1.3 68.7 + - - +
272D PRO* 3.5 7.6 - - - +
276D SER* 3.8 14.6 - - - -
277D ALA* 3.6 31.6 - - + +
281D VAL 3.3 30.7 - - - +
282D LYS* 3.7 2.7 - - - -
283D ALA* 3.7 22.9 - - + +
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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