Contacts of the strand formed by residues 241 - 248 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207H VAL* 3.5 19.7 - - + +
208H GLU 3.0 4.0 + - - -
209H PHE* 3.3 9.3 + - - -
238H LYS* 3.6 24.7 + - + +
239H LEU 3.1 11.4 + - - -
240H ASN* 1.3 78.3 + - - +
242H LYS* 1.3 61.6 + - - +
258H ILE* 3.5 31.2 - - + -
259H GLU 3.3 14.1 - - - +
260H ALA* 5.0 1.7 - - - -
265H LYS* 5.9 1.2 + - - -
481H NAD 3.1 24.1 - - - -
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Residues in contact with LYS 242 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155H PHE* 5.9 1.4 - - - -
209H PHE* 3.7 28.0 - - + -
241H THR* 1.3 73.0 - - - +
243H VAL* 1.3 75.6 + - - +
244H THR* 3.4 18.5 + - + +
258H ILE* 3.3 3.6 - - - +
259H GLU* 2.7 42.7 + - + +
260H ALA 4.6 2.5 - - - +
261H ALA* 4.2 11.3 - - - +
481H NAD 3.7 10.2 + - - +
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Residues in contact with VAL 243 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155H PHE* 3.3 23.0 - - + -
158H ILE* 4.4 3.1 - - + -
182H VAL* 5.8 0.2 - - + -
184H ILE* 3.8 39.3 - - + -
207H VAL* 3.5 33.9 - - + -
242H LYS* 1.3 78.3 + - - +
244H THR* 1.3 60.4 + - - +
245H GLY 4.0 9.9 - - - +
256H VAL* 3.8 24.0 - - + -
257H SER 3.7 3.6 - - - -
258H ILE* 4.0 6.7 - - + -
481H NAD 3.2 20.3 + - - +
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Residues in contact with THR 244 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155H PHE* 3.8 13.8 - - - -
156H PRO 5.4 0.5 - - - +
242H LYS* 4.2 21.6 + - + +
243H VAL* 1.3 75.1 - - - +
245H GLY* 1.3 58.4 + - - +
257H SER* 2.6 44.8 + - - +
258H ILE 4.5 1.3 - - - -
259H GLU* 3.7 37.0 - - + +
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Residues in contact with GLY 245 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155H PHE* 4.8 0.4 - - - -
157H GLY* 6.4 0.4 - - - -
158H ILE* 4.2 15.9 - - - -
243H VAL* 3.6 1.9 - - - -
244H THR* 1.3 85.2 + - - +
246H ALA* 1.3 63.2 + - - +
247H THR* 5.6 0.4 - - - -
256H VAL* 3.5 4.3 - - - +
257H SER* 2.9 30.3 + - - +
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Residues in contact with ALA 246 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157H GLY 5.2 3.5 - - - +
158H ILE* 3.9 22.7 - - + +
165H ILE* 5.5 4.1 - - + +
245H GLY* 1.3 76.0 - - - +
247H THR* 1.3 70.8 + - - +
254H ILE* 4.3 4.9 - - + -
255H ASP 3.0 13.7 - - - +
256H VAL* 4.1 7.4 - - + -
274H LEU* 3.8 28.7 - - + -
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Residues in contact with THR 247 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165H ILE* 5.6 0.4 - - - -
245H GLY 5.6 0.2 - - - -
246H ALA* 1.3 84.2 - - - +
248H LYS* 1.3 63.7 + - - +
249H LYS* 3.4 8.7 + - - +
254H ILE* 3.8 3.3 - - - -
255H ASP* 2.9 39.7 + - - +
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Residues in contact with LYS 248 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161H ASP* 3.9 22.6 + - - -
163H ASP* 5.5 3.8 + - - -
164H THR* 4.0 15.6 + - + +
165H ILE* 4.7 14.7 - - + +
247H THR* 1.3 73.2 - - - +
249H LYS* 1.3 68.6 + - - +
252H GLY* 4.6 9.0 - - - +
253H LYS 3.9 4.5 - - - +
254H ILE* 4.2 22.2 - - + +
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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