Contacts of the strand formed by residues 244 - 252 (chain A) in PDB entry 2ZB8
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 MET 244 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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225A VAL* 3.4 19.3 - - + +
226A ASP 4.3 1.3 - - - +
227A VAL 4.5 1.1 - - - -
228A TYR* 3.8 20.4 - - + +
240A VAL* 3.3 16.6 - - + +
241A ILE* 3.1 25.7 + - - +
242A SER 3.4 0.4 - - - -
243A GLN* 1.3 79.7 - - - +
245A ASN* 1.3 63.4 - - - +
248A SER* 3.3 31.4 - - - +
249A HIS 3.7 24.5 - - - +
250A ILE* 3.7 28.0 - - + -
280A ARG* 2.7 34.3 + - - -
282A ILE* 3.7 9.9 - - + -
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Residues in contact with ASN 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223A ALA 3.1 20.8 + - - +
224A GLY* 3.4 15.2 - - - -
225A VAL 2.9 20.1 + - - +
226A ASP* 2.8 28.6 + - - +
243A GLN 4.3 0.7 - - - +
244A MET* 1.3 77.0 - - - +
246A GLU* 1.3 71.0 + - + +
247A ASN 3.4 0.3 + - - -
248A SER* 2.7 25.4 + - - -
280A ARG* 4.5 2.7 - - - +
282A ILE* 3.8 6.1 - - - +
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Residues in contact with GLU 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245A ASN* 1.3 80.3 - - + +
247A ASN* 1.3 80.3 + - - +
248A SER* 4.2 0.3 - - - -
280A ARG* 3.5 23.5 - - + +
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Residues in contact with ASN 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246A GLU* 1.3 82.6 + - - +
248A SER* 1.3 65.3 + - - +
249A HIS* 3.4 18.0 + - + -
280A ARG 2.8 12.3 + - - -
281A ASN* 2.3 49.2 + - - +
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Residues in contact with SER 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A VAL 3.7 14.4 - - - -
226A ASP* 3.2 20.4 - - - +
244A MET* 3.3 16.7 - - - +
245A ASN* 2.7 23.9 + - - -
246A GLU 3.2 1.9 - - - -
247A ASN* 1.3 83.8 - - - +
249A HIS* 1.3 66.2 + - - +
281A ASN 4.0 1.4 + - - +
282A ILE* 3.1 18.4 - - - +
283A THR 3.2 21.1 + - - -
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Residues in contact with HIS 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A LYS 3.6 15.7 - - - +
148A GLY* 4.2 9.6 + - - +
149A HIS* 3.1 52.3 + + + +
156A LYS* 6.1 0.6 + - - -
226A ASP 3.1 6.5 + - - +
227A VAL* 3.4 8.0 - - + +
228A TYR 3.0 22.9 + - - -
244A MET* 3.7 1.4 - - - +
247A ASN 3.4 17.7 + - - -
248A SER* 1.3 81.0 - - - +
250A ILE* 1.3 65.5 + - - +
283A THR* 3.5 36.3 + - + +
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Residues in contact with ILE 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A LYS* 5.0 5.2 - - - +
228A TYR* 3.4 22.9 - - + +
230A ASP* 4.1 12.1 - - + +
241A ILE* 3.8 35.0 - - + -
244A MET* 3.7 15.3 - - + -
249A HIS* 1.3 73.7 - - - +
251A ILE* 1.3 69.6 + - - +
252A LEU* 3.3 9.7 + - + +
277A GLN* 5.3 2.0 - - + -
282A ILE* 3.6 27.8 - - + -
283A THR* 2.8 17.4 + - - +
284A ARG* 4.0 36.7 - - + +
285A GLU 4.4 3.5 + - - +
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Residues in contact with ILE 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A GLY* 3.8 28.0 - - - +
144A ILE* 3.7 28.9 - - + -
147A LYS* 4.0 24.2 - - + +
148A GLY* 3.9 9.2 - - - -
158A MET* 4.8 0.4 - - + -
227A VAL* 3.5 28.0 - - + -
228A TYR 2.7 10.5 + - - +
229A PHE* 3.8 33.2 - - + -
230A ASP* 2.9 30.0 + - - +
249A HIS 3.9 0.4 + - - +
250A ILE* 1.3 71.1 - - - +
252A LEU* 1.3 58.2 + - - +
253A CYS* 3.0 8.1 + - - +
287A PHE* 4.8 7.6 - - + -
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Residues in contact with LEU 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A LYS* 5.9 0.4 - - - +
230A ASP* 4.2 7.0 - - + +
250A ILE* 3.3 7.8 + - + +
251A ILE* 1.3 69.2 - - - +
253A CYS* 1.3 63.8 + - - +
254A GLY 3.7 0.4 - - - +
255A GLN* 3.4 36.1 - - + +
265A TYR* 4.1 13.0 + - - +
266A PRO* 3.9 28.7 - - + -
284A ARG* 4.0 40.2 - - + +
285A GLU 3.4 28.5 + - - +
286A ARG* 4.5 6.1 - - - +
287A PHE* 3.6 25.1 + - - +
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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