Contacts of the helix formed by residues 249 - 259 (chain A) in PDB entry 1ZEB
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 ASN 249 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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247A VAL* 4.2 0.3 - - - +
248A TRP* 1.3 97.5 - - + +
250A ARG* 1.3 60.7 + - - +
251A THR* 3.2 5.5 + - - +
252A GLU* 3.1 20.0 + - - +
253A LEU 3.0 22.7 + - - -
269A PHE* 3.6 14.0 - - - -
283A THR 5.6 0.2 - - - +
284A LEU* 3.4 21.1 - - + +
803A NAG 1.5 64.6 + - + +
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Residues in contact with ARG 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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249A ASN* 1.3 71.2 - - - +
251A THR* 1.3 65.0 + - - +
253A LEU* 3.2 9.0 + - + +
254A MET* 2.9 58.9 + - + +
269A PHE* 4.3 0.6 - - - -
280A ARG* 4.6 1.2 - - - +
282A SER* 3.2 29.5 + - - -
283A THR* 3.7 8.7 + - - +
284A LEU* 2.9 22.8 + - - +
285A ASP 3.4 18.4 - - - +
286A PRO* 4.0 13.9 - - + -
290A GLU* 2.9 37.3 + - - +
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Residues in contact with THR 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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249A ASN* 3.2 16.3 + - - -
250A ARG* 1.3 81.8 - - + +
252A GLU* 1.3 65.2 + - - +
254A MET* 3.4 26.1 + - + +
255A GLN* 3.1 22.2 + - - +
283A THR 4.4 14.0 + - - +
803A NAG 4.3 13.3 + - + +
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Residues in contact with GLU 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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245A ARG* 3.0 44.0 + - - +
247A VAL* 3.7 23.4 - - + +
248A TRP 5.6 0.2 - - - +
249A ASN* 3.1 22.7 + - - +
251A THR* 1.3 77.0 + - - +
253A LEU* 1.3 65.6 + - - +
255A GLN* 3.4 13.7 + - - +
256A ALA* 3.0 11.4 + - - +
803A NAG 3.4 38.6 + - - +
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Residues in contact with LEU 253 (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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200A LEU* 3.7 27.1 - - + -
247A VAL* 4.0 8.7 - - + +
249A ASN 3.0 14.4 + - - +
250A ARG* 3.3 9.4 - - + +
252A GLU* 1.3 77.2 - - - +
254A MET* 1.3 58.4 + - + +
256A ALA* 3.3 2.4 + - - +
257A SER* 2.8 30.0 + - - -
265A LEU* 3.7 18.6 - - + -
269A PHE* 3.8 12.6 - - + -
286A PRO* 3.7 36.1 - - + -
290A GLU* 4.8 2.0 - - + +
291A MET* 4.3 7.9 - - + -
294A ALA* 3.8 25.6 - - + -
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Residues in contact with MET 254 (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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250A ARG* 2.9 51.9 + - + +
251A THR* 3.4 26.0 - - + +
253A LEU* 1.3 77.6 - - + +
255A GLN* 1.3 63.2 + - - +
257A SER* 2.9 23.0 + - - -
258A LEU* 3.4 18.2 + - + +
297A ARG* 5.0 5.6 - - - +
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Residues in contact with GLN 255 (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 ARG* 3.0 34.9 + - - +
251A THR 3.1 10.4 + - - +
252A GLU* 3.7 15.6 + - - +
253A LEU 3.4 0.2 - - - -
254A MET* 1.3 80.6 - - - +
256A ALA* 1.3 62.6 + - - +
258A LEU* 3.3 6.3 + - - +
259A ASP* 3.2 25.2 + - + +
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Residues in contact with ALA 256 (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 ARG* 3.6 23.9 - - - +
247A VAL* 4.3 0.7 - - + -
252A GLU 3.0 17.7 + - - +
253A LEU 3.6 3.8 - - - +
255A GLN* 1.3 77.5 - - - +
257A SER* 1.3 56.8 + - - +
259A ASP* 3.0 27.6 + - - +
262A VAL* 3.7 16.2 - - + +
265A LEU* 3.6 31.4 - - + +
298A LEU* 5.7 0.9 - - - +
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Residues in contact with SER 257 (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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253A LEU 2.8 17.6 + - - -
254A MET* 2.9 20.4 + - - -
256A ALA* 1.3 73.1 - - - +
258A LEU* 1.3 55.5 + - - +
265A LEU* 4.7 7.8 - - - +
294A ALA* 3.9 28.0 - - - +
297A ARG* 3.0 44.9 + - - +
298A LEU* 4.7 4.8 + - - -
301A ARG* 3.0 20.4 + - - -
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Residues in contact with LEU 258 (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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254A MET* 3.4 18.4 + - + +
255A GLN* 3.3 6.1 + - - +
256A ALA 3.1 0.6 - - - -
257A SER* 1.3 76.5 + - - +
259A ASP* 1.3 59.2 + - - +
260A PRO* 3.3 11.6 - - - +
297A ARG* 3.8 38.4 - - + +
301A ARG* 4.2 8.5 + - - +
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Residues in contact with ASP 259 (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 ARG* 3.8 12.1 + - - -
255A GLN* 3.2 19.5 + - + +
256A ALA* 3.0 10.5 + - - +
257A SER 3.5 0.2 - - - -
258A LEU* 1.3 75.6 - - - +
260A PRO* 1.3 99.5 - - - +
261A SER* 3.2 7.0 + - - -
262A VAL* 3.1 37.7 + - + +
301A ARG* 4.6 4.9 + - - -
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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