Contacts of the strand formed by residues 256 - 261 (chain C) in PDB entry 3MSS
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 VAL 256 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C STI 3.8 32.8 - - + +
247C LYS* 3.5 5.7 - - - +
248C LEU* 2.7 50.5 + - + +
253C TYR* 3.5 34.9 - - + +
254C GLY 2.8 9.3 + - - +
255C GLU* 1.3 77.5 - - - +
257C TYR* 1.3 58.5 + - - +
269C ALA* 4.4 0.4 - - + -
270C VAL 3.3 16.8 - - - +
271C LYS* 4.1 22.4 - - + -
382C PHE 6.1 0.2 - - - +
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Residues in contact with TYR 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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244C MET* 3.6 28.7 - - + -
245C LYS 3.5 20.4 - - - +
246C HIS* 3.4 2.5 - - - +
247C LYS* 3.6 37.2 + - + +
248C LEU* 4.3 4.4 - - - +
255C GLU* 3.0 30.6 + - - -
256C VAL* 1.3 77.3 - - - +
258C GLU* 1.3 69.6 + - - +
259C GLY 3.6 0.2 + - - -
269C ALA* 3.6 3.8 - - - -
270C VAL* 2.9 32.3 + - - +
272C THR* 3.6 31.2 - - + -
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Residues in contact with GLU 258 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244C MET* 3.9 0.7 - - - -
245C LYS* 2.8 58.4 + - + +
246C HIS* 2.8 16.1 + - + +
248C LEU* 3.8 21.0 - - + +
257C TYR* 1.3 75.5 - - - +
259C GLY* 1.3 62.1 + - - +
267C THR* 3.4 31.7 + - + +
268C VAL 3.7 4.7 - - - +
270C VAL* 5.1 0.2 - - - -
317C PHE* 4.3 15.9 - - + -
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Residues in contact with GLY 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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242C ILE* 4.2 7.2 - - - -
243C THR 3.2 11.9 - - - -
244C MET* 4.5 1.3 - - - -
245C LYS* 4.3 1.6 - - - -
257C TYR 3.6 1.4 + - - -
258C GLU* 1.3 75.6 - - - +
260C VAL* 1.3 65.1 + - - +
267C THR* 3.3 8.3 - - - +
268C VAL* 2.8 45.3 + - - +
270C VAL* 4.5 3.1 - - - -
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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
----------------------------------------------------------
242C ILE* 3.3 4.3 - - - +
243C THR* 2.8 46.7 + - + +
245C LYS* 3.2 35.9 - - + +
259C GLY* 1.3 77.5 - - - +
261C TRP* 1.3 69.6 + - - +
262C LYS* 3.1 16.4 + - + +
265C SER* 4.4 6.7 - - - -
266C LEU 3.5 15.7 - - - +
267C THR* 4.6 10.3 - - + +
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Residues in contact with TRP 261 (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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237C MET* 3.4 28.0 - - + -
241C ASP* 3.6 37.8 + - + +
242C ILE* 4.2 9.2 - - + -
259C GLY 4.1 0.6 - - - -
260C VAL* 1.3 71.0 - - - +
262C LYS* 1.3 66.1 + - - +
263C LYS* 4.0 13.9 - - + +
264C TYR* 3.0 50.5 + + - -
265C SER 3.0 8.8 + - - -
266C LEU* 2.8 36.5 + - + +
268C VAL* 4.1 16.7 - - + +
302C LEU* 3.9 38.1 - - + -
314C ILE* 5.1 2.7 - - + -
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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