Contacts of the helix formed by residues 251 - 262 (chain A) in PDB entry 2ZOQ
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 LEU 251 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200A PHE* 5.0 0.2 - - + -
201A LEU* 4.0 25.4 - - + -
216A MET* 5.3 1.2 - - - +
249A HIS* 3.6 13.2 + - + -
250A TYR* 1.3 93.6 - - + +
252A ASP* 1.3 64.5 + - - +
253A GLN* 2.9 5.3 - - - +
254A LEU* 2.7 28.8 + - + +
255A ASN* 2.9 20.4 + - - +
280A TYR* 3.3 44.2 - - + +
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Residues in contact with ASP 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A GLY* 3.3 5.7 - - - -
248A LYS* 2.6 43.2 + - - +
249A HIS* 2.9 37.1 + - + +
250A TYR 2.6 8.3 + - - -
251A LEU* 1.3 73.6 - - - +
253A GLN* 1.3 50.7 + - - +
255A ASN* 2.8 19.7 + - - +
256A HIS* 2.7 48.6 + - - +
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Residues in contact with GLN 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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208A ARG* 3.0 49.8 + - + +
209A TRP* 3.2 6.0 + - - -
211A ARG* 4.6 4.7 + - + +
216A MET* 4.2 22.4 - - + -
245A PHE* 3.0 34.7 + - - +
246A PRO 2.1 31.2 - - - +
247A GLY* 4.3 2.0 - - - -
249A HIS 3.1 3.7 + - - +
250A TYR* 4.7 0.7 - - - -
251A LEU 4.3 6.1 - - - +
252A ASP* 1.3 79.3 - - - +
254A LEU* 1.3 62.8 + - - +
256A HIS* 3.2 13.0 + - - +
257A ILE* 3.2 19.7 + - + +
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Residues in contact with LEU 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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200A PHE* 4.6 3.4 - - + -
213A PRO* 4.2 15.5 - - + +
216A MET* 3.8 26.9 - - + +
217A LEU* 3.4 40.4 - - + -
251A LEU* 2.7 23.8 + - + +
253A GLN* 1.3 80.7 - - - +
255A ASN* 1.3 58.9 + - - +
257A ILE* 3.6 5.7 + - + +
258A LEU* 3.3 33.8 + - + +
280A TYR* 3.6 35.9 - - + -
281A LEU* 4.8 2.5 - - + -
313A PHE* 5.5 0.7 - - + -
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Residues in contact with ASN 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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249A HIS* 5.7 1.2 - - - -
251A LEU* 2.9 21.3 + - - +
252A ASP* 2.8 22.1 + - - +
254A LEU* 1.3 77.8 - - - +
256A HIS* 1.3 62.1 + - - +
257A ILE 3.2 0.7 - - - -
258A LEU* 3.5 5.0 + - - +
259A GLY* 3.0 19.9 + - - -
280A TYR* 2.4 36.9 + - - -
284A LEU* 4.2 12.3 - - - +
287A LYS* 3.9 9.3 + - - +
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Residues in contact with HIS 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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244A ILE 4.7 0.9 - - - -
245A PHE* 3.7 28.5 - - - -
246A PRO* 3.1 36.7 - - + +
247A GLY 4.1 9.9 + - - -
248A LYS* 5.4 7.2 - - - -
252A ASP* 2.7 41.1 + - - +
253A GLN* 3.2 10.1 + - - +
255A ASN* 1.3 72.9 - - - +
257A ILE* 1.3 63.8 + - - +
259A GLY* 3.3 8.9 + - - -
260A ILE* 3.6 10.0 + - - +
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Residues in contact with ILE 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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211A ARG 3.6 20.9 - - - +
213A PRO* 3.7 28.7 - - + -
216A MET* 4.6 3.4 - - + -
229A TRP* 3.6 28.9 - - + +
245A PHE* 3.9 20.9 - - + -
253A GLN* 3.2 18.5 + - - +
254A LEU* 3.6 10.1 - - - +
255A ASN 3.2 0.4 - - - -
256A HIS* 1.3 75.0 - - - +
258A LEU* 1.3 69.5 + - + +
259A GLY 3.0 1.1 - - - -
260A ILE* 2.9 21.0 + - - +
261A LEU* 2.9 38.3 + - + +
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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 LEU* 3.3 26.5 + - + +
255A ASN* 4.0 7.0 - - - +
257A ILE* 1.3 81.6 - - + +
259A GLY* 1.3 58.1 - - - +
261A LEU* 4.4 1.8 - - + +
262A GLY* 2.8 37.5 + - - +
263A SER* 5.5 1.1 - - - +
264A PRO* 4.0 33.2 - - + -
281A LEU* 4.2 14.1 - - + -
284A LEU* 3.4 34.3 - - + -
287A LYS* 3.4 17.8 - - - +
313A PHE* 4.2 17.9 - - + -
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Residues in contact with GLY 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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255A ASN 3.0 11.5 + - - -
256A HIS* 3.7 6.1 - - - -
257A ILE 3.0 1.8 - - - -
258A LEU* 1.3 80.6 - - - +
260A ILE* 1.3 60.4 + - - +
262A GLY* 4.6 1.0 + - - -
287A LYS* 3.1 22.5 - - - +
288A THR 4.7 3.5 - - - +
290A VAL* 3.6 15.9 - - - +
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Residues in contact with ILE 260 (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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244A ILE* 3.3 32.3 - - + +
245A PHE* 3.3 31.6 - - + +
256A HIS 3.6 4.5 + - - +
257A ILE 2.9 2.4 + - - -
259A GLY* 1.3 79.5 - - - +
261A LEU* 1.3 63.5 + - + +
262A GLY 3.2 1.6 - - - -
289A LYS* 3.6 3.1 - - - +
290A VAL* 3.0 34.5 + - + +
292A TRP* 3.8 33.4 - - + -
295A LEU* 4.0 27.1 - - + -
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Residues in contact with LEU 261 (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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229A TRP* 3.7 25.1 - - + -
245A PHE* 4.4 5.6 - - + -
257A ILE* 2.9 28.8 + - + +
258A LEU* 4.5 2.5 - - + -
260A ILE* 1.3 88.1 - - + +
262A GLY* 1.3 68.1 + - - +
263A SER 4.8 1.6 - - - +
289A LYS* 3.3 27.9 - - - +
292A TRP* 4.4 12.1 - - + -
311A LEU 3.7 17.0 - - - +
313A PHE* 3.7 42.2 - - + +
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Residues in contact with GLY 262 (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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258A LEU* 2.8 26.1 + - - +
260A ILE 3.2 3.0 - - - -
261A LEU* 1.3 89.5 - - - +
263A SER* 1.3 67.5 + - - -
264A PRO* 3.4 5.9 - - - +
287A LYS* 3.0 15.3 - - - -
288A THR 3.7 16.6 + - - -
289A LYS 3.7 0.7 - - - -
313A PHE* 6.0 0.2 - - - -
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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