Contacts of the helix formed by residues 247 - 253 (chain A) in PDB entry 1Z6T
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 ASP 247 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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189A LYS* 3.1 31.6 + - - +
190A GLN 4.4 5.7 + - - +
245A VAL* 3.5 10.2 - - - +
246A TRP* 1.3 91.6 - - - +
248A SER* 1.3 65.0 + - - +
249A TRP* 3.5 34.6 + - + +
250A VAL* 3.1 27.2 + - + +
251A LEU 3.5 1.0 + - - -
269A VAL* 4.0 5.8 - - - -
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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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247A ASP* 1.3 72.5 - - - +
249A TRP* 1.3 61.8 + - - +
251A LEU* 3.2 11.6 + - - +
252A LYS 3.2 6.2 + - - -
268A SER 4.3 4.3 - - - -
269A VAL* 3.1 36.6 + - - +
271A ASP* 5.2 2.3 - - - +
272A SER* 3.2 38.9 + - - -
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Residues in contact with TRP 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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190A GLN 3.4 21.1 + - - -
191A ASP* 3.6 29.4 - - - -
192A LYS* 3.3 45.1 - - + +
195A LEU* 3.7 23.8 - - + -
220A ILE* 4.3 7.0 - - + -
247A ASP* 3.2 32.3 + - + +
248A SER* 1.3 81.9 + - - +
250A VAL* 1.3 75.5 + - + +
252A LYS* 3.4 20.5 + - - +
253A ALA* 3.6 5.7 + - + +
272A SER* 5.0 0.9 - - - -
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Residues in contact with VAL 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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187A VAL* 4.0 22.4 - - + -
188A GLY 5.7 1.1 - - - +
190A GLN* 4.8 12.6 - - + +
195A LEU* 3.8 16.4 - - + -
245A VAL* 4.3 11.2 - - + -
246A TRP* 5.5 1.3 - - + +
247A ASP* 3.1 23.4 + - + +
249A TRP* 1.3 113.2 - - + +
251A LEU* 1.3 61.5 + - - +
253A ALA* 3.2 11.4 + - - +
254A PHE* 3.2 27.8 - - + -
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Residues in contact with LEU 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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149A TRP* 3.5 37.9 - - + -
242A LEU* 4.0 19.7 - - + -
245A VAL* 3.9 22.0 - - + -
247A ASP 3.5 3.9 + - - +
248A SER 3.2 10.7 + - - +
250A VAL* 1.3 78.2 - - - +
252A LYS* 1.3 56.9 + - - +
254A PHE* 3.0 21.8 + - - +
255A ASP 3.3 8.1 + - - -
262A LEU* 4.1 13.5 - - + -
269A VAL* 3.2 30.5 - - + +
270A THR* 3.7 24.5 - - - +
273A VAL* 4.3 9.4 - - + -
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Residues in contact with LYS 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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224A LYS* 2.8 43.2 + - - +
248A SER 3.2 7.6 + - - +
249A TRP* 3.5 14.1 - - - +
250A VAL 3.3 0.2 - - - -
251A LEU* 1.3 69.6 - - - +
253A ALA* 1.3 62.2 + - - +
254A PHE 3.1 2.2 - - - -
255A ASP* 3.2 35.6 + - - +
272A SER* 3.5 38.8 - - - +
273A VAL* 4.3 2.2 - - + +
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Residues in contact with ALA 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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195A LEU* 3.7 22.2 - - + -
199A LEU* 4.3 11.1 - - + +
220A ILE* 4.2 18.8 - - + -
224A LYS* 3.5 35.3 - - + +
227A LEU* 4.4 5.2 - - - +
249A TRP* 3.6 5.2 + - + +
250A VAL 3.2 17.1 + - - +
252A LYS* 1.3 77.4 - - - +
254A PHE* 1.3 60.6 + - + +
256A SER* 4.4 1.0 + - - -
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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