Contacts of the strand formed by residues 253 - 260 (chain C) in PDB entry 3ASK
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 ARG 253 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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214C TRP* 3.7 57.1 - - + +
215C GLN* 5.0 4.4 - - - +
247C ARG 3.8 3.4 - - - -
248C GLU* 4.1 18.2 - - + +
252C ALA* 1.3 74.5 - - - +
254C GLU* 1.3 62.1 + - - +
255C LEU 3.8 2.3 + - - -
270C ARG* 4.3 7.8 + - - -
274C VAL* 3.5 31.4 - - + +
275C ASP* 3.2 36.8 + - - -
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Residues in contact with GLU 254 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214C TRP* 3.4 5.5 - - - -
245C ARG 3.7 0.5 - - - +
246C LYS* 3.3 7.8 - - - -
247C ARG* 2.8 79.2 + - + +
249C THR* 4.6 4.5 - - - +
252C ALA* 4.2 16.1 - - + +
253C ARG* 1.3 74.5 - - - +
255C LEU* 1.3 59.9 + - - +
256C TYR* 3.1 31.3 + - + +
270C ARG* 3.6 27.0 + - - +
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Residues in contact with LEU 255 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214C TRP* 3.9 15.9 - - + -
217C LEU* 3.9 31.6 - - + -
225C LEU* 4.5 4.9 - - + -
243C ILE* 4.0 30.7 - - + -
246C LYS* 4.2 7.9 - - + -
253C ARG 3.8 3.0 + - - -
254C GLU* 1.3 73.9 - - - +
256C TYR* 1.3 64.5 + - - +
270C ARG* 3.5 11.6 - - - +
271C ILE* 2.8 53.2 + - + +
274C VAL* 4.0 19.1 - - + -
277C VAL* 4.0 18.6 - - + -
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Residues in contact with TYR 256 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243C ILE* 3.7 5.5 - - - +
244C SER* 2.8 32.2 + - - +
245C ARG* 2.9 66.7 + - + +
247C ARG* 4.9 4.5 - - + -
254C GLU* 3.1 42.3 + - + -
255C LEU* 1.3 74.1 - - - +
257C ALA* 1.3 63.5 + - - +
268C ASP* 4.1 15.7 - - - +
269C CYS 3.1 7.0 - - - +
270C ARG* 3.5 47.7 + - + -
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Residues in contact with ALA 257 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225C LEU* 4.3 1.6 - - + -
241C ALA* 3.9 16.4 - - + -
242C GLU 3.2 16.8 - - - +
243C ILE* 3.7 14.1 - - + +
244C SER* 3.6 4.2 + - - -
255C LEU* 5.4 0.2 - - + -
256C TYR* 1.3 77.8 - - - +
258C ASN* 1.3 64.9 + - - +
259C VAL* 3.4 1.5 + - - +
268C ASP 4.2 0.9 - - - -
269C CYS* 2.8 38.1 + - - +
271C ILE* 4.1 16.1 - - + +
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Residues in contact with ASN 258 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241C ALA* 3.2 19.5 - - - -
242C GLU* 2.8 40.8 + - + +
244C SER* 4.1 13.7 - - - -
257C ALA* 1.3 69.6 - - - +
259C VAL* 1.3 63.5 + - - +
260C VAL* 3.5 6.6 + - + +
265C SER* 5.3 3.8 - - - -
266C LEU 3.9 5.6 - - - -
267C ASN* 3.3 27.5 + - - +
268C ASP* 3.1 19.8 + - - +
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Residues in contact with VAL 259 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225C LEU* 4.5 2.0 - - + -
227C TYR* 3.7 19.3 - - + -
239C TYR* 3.5 33.9 - - + -
240C ASP 3.8 3.8 - - - -
241C ALA* 3.8 8.1 - - + -
257C ALA 4.1 2.2 - - - +
258C ASN* 1.3 71.9 - - - +
260C VAL* 1.3 63.4 + - - +
261C LEU* 3.7 17.8 + - + -
265C SER* 3.6 1.2 - - - -
266C LEU* 2.8 39.0 + - + +
269C CYS* 3.6 35.4 - - + -
271C ILE* 4.2 9.4 - - + -
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Residues in contact with VAL 260 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144C ARG* 5.8 6.1 - - - +
149C GLY 4.5 5.9 - - - +
222C VAL* 6.5 0.7 - - + -
239C TYR* 3.8 12.8 - - - +
240C ASP* 2.8 37.7 + - + +
241C ALA* 4.7 1.3 - - - -
242C GLU 5.4 1.3 - - - +
258C ASN* 4.0 7.9 - - + +
259C VAL* 1.3 73.2 - - - +
261C LEU* 1.3 75.5 + - - +
263C ASP 5.6 2.5 - - - +
264C ASP 4.9 2.0 - - - +
265C SER* 4.0 20.2 - - - +
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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