Contacts of the strand formed by residues 265 - 270 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244C ILE* 5.8 0.4 - - + -
247C THR 3.7 3.6 - - - -
249C MET* 4.1 3.5 - - - +
264C GLY* 1.3 73.4 - - - -
266C PHE* 1.3 61.5 + - - +
267C VAL* 3.8 1.7 + - + -
285C ASP 3.6 0.7 - - - +
286C ILE* 3.2 6.1 - - - -
287C ILE* 2.8 55.8 + - + +
295C LEU* 5.3 0.6 - - + +
298C PHE* 3.3 34.1 - - + -
301C LEU* 4.3 11.0 - - + -
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Residues in contact with PHE 266 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246C GLY* 3.1 6.8 - - - -
247C THR* 2.9 51.2 + - - +
248C GLU 4.5 0.7 - - - +
249C MET* 3.6 35.1 - - + +
253C ILE* 4.1 25.4 - - + -
257C PHE* 4.9 10.8 - + - -
265C ALA* 1.3 73.1 - - - +
267C VAL* 1.3 67.5 + - - +
268C SER* 3.6 9.8 + - - -
284C GLY* 4.0 28.5 - - - -
285C ASP 3.8 1.8 - - - -
286C ILE* 3.9 10.1 - - + -
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Residues in contact with VAL 267 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244C ILE* 3.7 31.4 - - + -
245C LYS 3.8 5.2 - - - +
246C GLY* 4.4 0.4 - - - -
265C ALA* 4.5 2.2 - - + +
266C PHE* 1.3 76.1 - - - +
268C SER* 1.3 60.4 + - - +
269C GLU 3.7 13.5 - - - +
270C VAL* 3.8 13.7 - - + -
281C VAL* 4.4 2.2 - - + -
282C LYS 4.0 10.8 - - - +
283C ALA* 4.2 1.1 - - - -
284C GLY* 2.7 30.8 + - - -
285C ASP* 2.9 29.2 + - + +
287C ILE* 3.7 33.4 - - + -
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Residues in contact with SER 268 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245C LYS* 2.9 24.1 + - - +
246C GLY* 3.8 6.8 - - - -
247C THR* 5.5 4.3 - - - +
266C PHE* 3.6 14.0 + - - -
267C VAL* 1.3 73.3 - - - +
269C GLU* 1.3 65.4 + - - +
283C ALA* 3.3 17.9 - - - +
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Residues in contact with GLU 269 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244C ILE* 3.6 3.6 - - - -
245C LYS* 2.9 69.5 + - + +
267C VAL* 3.7 2.8 - - - +
268C SER* 1.3 83.0 - - - +
270C VAL* 1.3 71.3 + - - +
271C LEU* 3.5 22.0 - - + +
283C ALA* 4.5 2.7 - - - -
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Residues in contact with VAL 270 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243C GLY 3.6 3.1 - - - +
244C ILE* 3.7 12.1 - - + -
267C VAL* 3.8 3.4 - - + -
269C GLU* 1.3 81.3 - - - +
271C LEU* 1.3 67.8 + - - +
272C PRO* 3.5 8.0 - - - +
276C SER* 3.7 14.6 - - - -
277C ALA* 3.6 32.9 - - + +
281C VAL 3.2 35.4 - - - +
282C LYS* 3.7 17.5 - - - -
283C ALA* 3.7 4.3 - - - +
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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
------------------------------------------------------------
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