Contacts of the strand formed by residues 241 - 248 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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207E VAL* 3.7 11.0 - - - +
208E GLU 3.1 8.2 + - - +
209E PHE* 3.4 4.0 + - - -
238E LYS* 2.7 52.4 + - + +
239E LEU 3.8 5.6 - - - +
240E ASN* 1.3 83.3 - - - +
242E LYS* 1.3 59.3 + - - +
258E ILE* 4.7 10.8 - - + -
259E GLU 3.2 14.1 - - - +
260E ALA* 4.0 8.3 - - + -
261E ALA 3.8 0.9 - - - +
265E LYS* 5.3 6.5 - - + +
267E GLU* 5.2 4.0 - - - +
481E NAD 3.2 22.9 - - - -
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Residues in contact with LYS 242 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209E PHE* 3.9 27.8 - - + -
241E THR* 1.3 72.7 - - - +
243E VAL* 1.3 67.1 + - - +
244E THR* 3.5 23.7 + - + +
258E ILE* 3.2 5.1 - - - +
259E GLU* 2.7 51.5 + - + +
260E ALA 5.2 0.4 - - - +
261E ALA* 4.0 12.9 - - - +
481E NAD 3.7 9.9 - - - +
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Residues in contact with VAL 243 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155E PHE* 3.0 33.0 - - + -
158E ILE* 4.5 0.9 - - + -
184E ILE* 3.8 31.0 - - + -
207E VAL* 3.5 31.2 - - + -
242E LYS* 1.3 77.7 + - - +
244E THR* 1.3 57.4 + - - +
245E GLY 4.0 10.5 - - - +
256E VAL* 3.8 25.4 - - + -
257E SER 3.7 4.5 - - - +
258E ILE* 3.9 8.3 - - + -
481E NAD 3.2 20.1 + - - +
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Residues in contact with THR 244 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155E PHE* 3.7 12.7 - - - -
156E PRO 5.3 0.7 - - - +
242E LYS* 4.3 19.7 + - - +
243E VAL* 1.3 76.0 - - - +
245E GLY* 1.3 57.2 + - - +
257E SER* 2.5 42.6 + - - +
258E ILE 4.6 2.0 - - - -
259E GLU* 3.3 39.7 - - + +
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Residues in contact with GLY 245 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155E PHE* 4.7 0.2 - - - -
157E GLY* 6.1 1.1 - - - -
158E ILE* 4.2 15.5 - - - -
243E VAL* 3.6 1.5 - - - -
244E THR* 1.3 85.8 + - - +
246E ALA* 1.3 63.7 + - - +
256E VAL* 3.5 4.9 - - - +
257E SER* 2.9 29.9 + - - +
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Residues in contact with ALA 246 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157E GLY 4.7 7.0 + - - +
158E ILE* 3.9 22.6 - - + +
165E ILE* 5.6 3.6 - - + +
245E GLY* 1.3 76.4 - - - +
247E THR* 1.3 71.4 + - - +
254E ILE* 4.2 4.5 - - + -
255E ASP 3.0 12.8 - - - +
256E VAL* 4.1 8.3 - - + -
274E LEU* 3.7 30.1 - - + -
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Residues in contact with THR 247 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165E ILE* 5.7 0.2 - - - -
245E GLY 5.7 0.2 - - - -
246E ALA* 1.3 82.5 - - - +
248E LYS* 1.3 65.2 + - - +
249E LYS* 3.4 8.8 + - - +
254E ILE* 3.5 4.6 - - - -
255E ASP* 2.9 44.7 + - - +
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Residues in contact with LYS 248 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161E ASP* 5.8 0.7 - - - +
163E ASP* 4.9 2.4 + - - -
164E THR* 3.1 45.5 - - + +
165E ILE* 4.6 15.8 - - + +
247E THR* 1.3 72.2 - - - +
249E LYS* 1.3 65.8 + - - +
252E GLY* 2.8 35.9 + - - +
253E LYS 3.6 2.5 - - - -
254E ILE* 3.8 13.9 - - + +
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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