Contacts of the strand formed by residues 241 - 248 (chain F) 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 THR 241 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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207F VAL* 3.2 29.1 - - + +
208F GLU 3.0 21.9 + - - -
209F PHE* 3.3 5.1 + - - -
238F LYS* 3.6 19.3 + - + +
239F LEU 3.1 13.0 + - - -
240F ASN* 1.3 80.0 + - - +
242F LYS* 1.3 61.7 + - - +
258F ILE* 3.8 28.0 - - + -
259F GLU 3.5 14.8 - - - +
260F ALA* 5.0 1.0 - - - -
261F ALA 4.0 0.7 - - - +
265F LYS* 6.1 1.0 - - - -
267F GLU* 5.8 1.1 - - - +
481F NAD 3.5 0.7 - - - -
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Residues in contact with LYS 242 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209F PHE* 3.5 34.1 - - + -
241F THR* 1.3 74.8 - - - +
243F VAL* 1.3 65.8 + - - +
244F THR* 3.7 9.9 + - - +
258F ILE* 3.3 3.6 - - - -
259F GLU* 2.8 71.0 + - + +
260F ALA 3.6 13.6 + - - +
261F ALA* 3.9 10.1 + - - +
263F GLY* 4.3 6.5 - - - -
481F NAD 3.6 9.2 - - - +
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Residues in contact with VAL 243 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155F PHE* 3.4 8.9 - - + -
158F ILE* 4.1 7.6 - - + -
182F VAL* 5.4 0.2 - - + -
184F ILE* 3.8 48.7 - - + -
207F VAL* 3.9 26.9 - - + -
242F LYS* 1.3 78.7 - - - +
244F THR* 1.3 62.3 + - - +
245F GLY 3.8 10.1 - - - +
256F VAL* 3.5 31.4 - - + -
257F SER 3.4 4.5 - - - +
258F ILE* 4.0 3.4 - - + -
481F NAD 3.1 20.8 + - - +
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Residues in contact with THR 244 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155F PHE* 4.0 14.4 - - - -
156F PRO 5.2 1.4 - - - +
242F LYS* 4.0 9.9 + - - -
243F VAL* 1.3 76.9 + - - +
245F GLY* 1.3 55.6 + - - +
257F SER* 2.6 24.8 + - - -
258F ILE 5.4 0.2 - - - -
259F GLU* 3.3 35.1 + - - +
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Residues in contact with GLY 245 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157F GLY 6.2 0.4 - - - -
158F ILE* 4.0 15.7 - - - -
243F VAL* 3.8 2.4 - - - +
244F THR* 1.3 82.0 - - - +
246F ALA* 1.3 62.8 + - - +
256F VAL* 3.4 8.3 - - - +
257F SER* 2.8 34.3 + - - -
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Residues in contact with ALA 246 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157F GLY 5.4 2.9 - - - +
158F ILE* 4.0 18.6 - - + +
165F ILE* 4.9 5.4 - - + -
245F GLY* 1.3 78.1 - - - +
247F THR* 1.3 68.5 + - - +
254F ILE* 4.0 7.9 - - + -
255F ASP 3.0 11.9 - - - +
256F VAL* 4.6 2.5 - - + -
257F SER* 5.3 0.2 - - - -
274F LEU* 3.6 30.7 - - + -
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Residues in contact with THR 247 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165F ILE* 6.0 0.4 - - - -
246F ALA* 1.3 81.4 + - - +
248F LYS* 1.3 75.5 + - - +
249F LYS* 3.8 4.7 + - + +
254F ILE* 3.6 4.8 - - - -
255F ASP* 3.0 36.2 + - - +
257F SER* 5.5 2.1 + - - -
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Residues in contact with LYS 248 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159F THR 5.6 0.9 - - - -
161F ASP* 2.8 28.7 + - - -
163F ASP* 5.9 0.6 + - - -
164F THR* 4.1 11.7 + - - +
165F ILE* 4.0 25.6 - - + -
247F THR* 1.3 89.6 - - - +
249F LYS* 1.3 63.4 + - - +
252F GLY 6.1 1.3 - - - -
253F LYS 3.6 7.9 - - - +
254F ILE* 4.7 7.4 - - + -
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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