Contacts of the strand formed by residues 254 - 260 (chain C) in PDB entry 1ZMC
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 ILE 254 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164C THR* 3.6 25.6 - - - +
165C ILE* 4.1 13.2 - - + -
246C ALA* 4.5 2.5 - - + -
247C THR 3.5 13.7 - - - +
248C LYS* 4.2 10.5 - - + -
252C GLY 4.1 6.5 - - - +
253C LYS* 1.3 79.3 - - - +
255C ASP* 1.3 72.2 + - - +
256C VAL* 4.4 0.7 - - + -
269C ILE 3.5 0.9 - - - +
270C THR* 3.0 6.4 - - - -
271C CYS* 2.9 41.0 + - - +
272C ASP 3.5 24.5 - - - +
273C VAL 4.0 0.7 - - - +
274C LEU* 3.7 37.0 - - + +
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Residues in contact with ASP 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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246C ALA* 3.1 4.3 - - - +
247C THR* 2.9 46.7 + - - +
249C LYS* 2.7 44.0 + - + +
253C LYS 4.2 0.4 - - - -
254C ILE* 1.3 72.0 - - - +
256C VAL* 1.3 61.5 + - - +
257C SER* 4.0 3.2 + - - +
268C VAL* 3.6 20.5 - - + +
269C ILE 3.2 1.8 - - - -
270C THR* 2.8 21.1 + - - +
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Residues in contact with VAL 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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182C VAL* 4.3 15.7 - - + -
184C ILE* 5.4 0.9 - - + -
243C VAL* 3.7 29.4 - - + -
245C GLY 3.6 3.6 - - - +
246C ALA* 4.1 8.5 - - + -
254C ILE* 4.4 1.8 - - + -
255C ASP* 1.3 75.9 - - - +
257C SER* 1.3 63.6 + - - +
258C ILE* 3.8 12.9 + - + +
268C VAL* 3.3 5.0 - - - -
269C ILE* 2.4 54.7 + - + +
271C CYS* 4.1 15.5 - - - -
274C LEU* 3.6 29.6 - - + -
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Residues in contact with SER 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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243C VAL* 3.4 6.4 - - - +
244C THR* 2.9 42.6 + - - -
245C GLY 2.8 17.8 + - - +
246C ALA* 5.3 0.2 - - - -
255C ASP* 4.0 3.7 + - - +
256C VAL* 1.3 73.8 - - - +
258C ILE* 1.3 64.2 + - - +
267C GLU 3.7 7.6 - - - -
268C VAL* 4.1 12.8 - - - +
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Residues in contact with ILE 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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207C VAL* 4.3 10.3 - - + -
238C LYS* 3.4 34.3 - - + -
241C THR* 3.5 19.3 - - + -
242C LYS 3.3 5.6 - - - +
243C VAL* 3.9 21.1 - - + -
244C THR* 4.4 0.9 - - - +
256C VAL* 4.1 14.4 - - + +
257C SER* 1.3 81.2 - - - +
259C GLU* 1.3 62.4 + - - +
266C ALA* 3.5 3.6 - - - +
267C GLU* 2.7 69.6 + - + +
268C VAL 4.7 0.2 - - - +
269C ILE* 4.3 14.4 - - + -
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Residues in contact with GLU 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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241C THR* 2.9 10.7 - - - +
242C LYS* 2.7 41.7 + - + +
244C THR* 3.7 25.4 - - + +
258C ILE* 1.3 77.0 - - - +
260C ALA* 1.3 65.1 + - - +
263C GLY* 4.3 6.4 - - - -
264C GLY 3.3 25.4 + - - +
265C LYS* 4.1 4.3 - - - -
266C ALA* 4.3 14.5 - - + +
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Residues in contact with ALA 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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240C ASN 3.6 7.9 - - - +
241C THR* 4.3 1.8 - - - +
242C LYS* 4.2 3.0 - - - +
259C GLU* 1.3 79.9 - - - +
261C ALA* 1.3 66.9 + - - +
262C SER* 4.2 9.4 - - - +
263C GLY* 2.9 31.6 + - - +
264C GLY 2.9 11.3 + - - +
265C LYS* 4.0 22.8 - - + +
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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