Contacts of the strand formed by residues 265 - 270 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244E ILE* 5.8 0.4 - - + -
247E THR 3.7 4.0 - - - -
249E MET* 4.4 2.9 - - - -
264E GLY* 1.3 72.5 - - - -
266E PHE* 1.3 63.4 + - - +
267E VAL* 3.7 1.7 + - + -
285E ASP 3.6 0.7 - - - +
286E ILE* 3.2 6.7 - - - +
287E ILE* 2.8 54.4 + - + +
295E LEU* 5.2 0.8 - - + +
298E PHE* 3.3 33.7 - - + -
301E LEU* 4.4 11.2 - - + -
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Residues in contact with PHE 266 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246E GLY* 3.1 5.2 - - - -
247E THR* 2.9 47.2 + - - +
248E GLU 4.5 4.9 - - - +
249E MET* 3.6 31.3 - - + +
253E ILE* 4.2 24.2 - - + -
257E PHE* 5.0 10.8 - + - -
264E GLY 4.2 0.6 + - - -
265E ALA* 1.3 71.8 - - - +
267E VAL* 1.3 68.6 + - - +
268E SER* 4.9 9.9 - - - -
284E GLY* 3.9 28.3 - - - -
285E ASP 3.7 1.6 - - - -
286E ILE* 3.9 11.4 - - + -
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Residues in contact with VAL 267 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244E ILE* 3.7 32.8 - - + -
245E LYS 3.8 5.6 - - - +
246E GLY* 4.4 0.9 - - - -
265E ALA* 4.4 2.2 - - + +
266E PHE* 1.3 75.7 - - - +
268E SER* 1.3 59.4 + - - +
269E GLU 3.7 13.7 - - - +
270E VAL* 3.8 13.0 - - + -
281E VAL* 4.6 2.5 - - + -
282E LYS 4.1 10.5 - - - +
283E ALA* 4.2 0.9 - - - -
284E GLY* 2.6 31.2 + - - -
285E ASP* 2.9 28.1 + - + +
287E ILE* 3.8 32.8 - - + -
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Residues in contact with SER 268 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245E LYS* 2.9 25.0 + - - +
246E GLY* 3.9 6.3 - - - -
247E THR* 5.3 3.6 + - - -
266E PHE* 3.6 13.3 + - - -
267E VAL* 1.3 73.3 - - - +
269E GLU* 1.3 61.6 + - - +
283E ALA* 3.4 17.6 - - - +
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Residues in contact with GLU 269 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244E ILE* 3.6 3.1 - - - -
245E LYS* 2.8 72.4 + - + +
267E VAL* 3.7 4.4 - - - +
268E SER* 1.3 82.2 - - - +
270E VAL* 1.3 71.7 + - - +
271E LEU* 3.5 20.9 + - + +
272E PRO* 5.8 1.2 - - - +
283E ALA* 4.5 3.1 - - - -
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Residues in contact with VAL 270 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243E GLY 3.6 2.9 - - - +
244E ILE* 3.7 13.7 - - + -
267E VAL* 3.8 2.9 - - + -
269E GLU* 1.3 79.6 - - - +
271E LEU* 1.3 67.1 + - - +
272E PRO* 3.5 6.9 - - - +
276E SER* 3.8 13.7 - - - -
277E ALA* 3.6 32.3 - - + +
281E VAL 3.3 29.8 - - - +
282E LYS* 3.7 3.8 - - - -
283E ALA* 3.7 23.4 - - + +
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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