Contacts of the helix formed by residues 262 - 271 (chain B) in PDB entry 2ZSU
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 262 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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272A MET 4.6 8.8 - - - +
274A ARG* 2.9 42.5 + - + +
277A VAL* 4.5 17.2 - - - +
224B PHE* 5.3 0.8 - - - -
260B TYR 3.4 3.4 + - - +
261B TYR* 1.3 84.1 - - - +
263B PRO* 1.3 63.4 - - - +
264B ASP* 3.1 9.5 + - - +
265B LYS* 3.0 53.4 + - + +
266B HIS 3.4 0.9 + - - -
268B THR* 5.7 1.6 - - - +
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Residues in contact with PRO 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274A ARG* 4.0 14.4 - - - +
72B LEU* 3.8 23.1 - - + -
248B VAL* 3.7 17.0 - - + +
250B ALA* 4.0 15.6 - - - +
253B GLY* 4.1 16.6 - - - -
258B LEU* 3.4 23.6 - - + -
261B TYR* 3.3 32.1 - - + +
262B ASP* 1.3 84.1 - - - +
264B ASP* 1.3 63.2 + - - +
265B LYS 3.2 1.2 + - - -
266B HIS* 3.6 7.4 + - - +
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Residues in contact with ASP 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274A ARG* 3.0 20.3 + - - +
250B ALA* 3.5 27.4 - - - +
254B LYS* 4.6 14.5 - - - +
262B ASP* 3.1 11.0 + - - +
263B PRO* 1.3 78.8 - - - +
265B LYS* 1.3 65.2 + - + +
266B HIS 3.6 1.1 - - - -
267B GLU* 4.5 3.3 - - - +
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Residues in contact with LYS 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221A TYR* 4.3 20.0 - - - +
246A MET* 6.0 1.8 - - - +
270A PHE* 3.9 19.2 + - - +
277A VAL* 5.5 4.5 - - + -
262B ASP* 3.0 34.8 + - + +
264B ASP* 1.3 88.9 - - + +
266B HIS* 1.3 62.7 + - - +
267B GLU* 3.1 18.7 + - - +
268B THR* 2.7 57.0 + - - +
269B LEU* 4.0 0.5 + - - +
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Residues in contact with HIS 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B PRO* 4.4 6.3 - - + -
245B PHE* 2.7 27.2 + + - -
246B MET 3.3 27.1 - - - -
247B LYS* 4.0 1.1 - - - -
248B VAL* 3.4 42.6 - - + +
261B TYR* 2.7 25.2 + - - +
262B ASP 3.4 6.8 + - - -
263B PRO 3.6 3.9 + - - +
264B ASP 3.6 0.6 - - - -
265B LYS* 1.3 76.2 - - - +
267B GLU* 1.3 59.1 + - - +
269B LEU* 2.9 51.4 + - + +
270B PHE* 3.5 15.1 - + - -
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Residues in contact with GLU 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267A GLU* 3.5 33.5 - - + +
268A THR* 3.7 15.6 - - - +
246B MET* 5.8 2.9 - - + +
264B ASP 4.5 2.8 - - - +
265B LYS* 3.5 25.6 + - - +
266B HIS* 1.3 77.7 + - - +
268B THR* 1.3 76.3 + - + +
269B LEU 3.1 1.8 + - - -
270B PHE* 3.4 22.1 + - - -
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Residues in contact with THR 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267A GLU 3.3 20.0 - - - +
268A THR* 4.0 10.2 - - - +
270A PHE* 3.8 10.3 + - + -
271A GLN* 3.4 43.9 + - - +
272A MET 4.9 0.7 + - - -
262B ASP* 5.7 1.9 - - - +
265B LYS* 2.7 51.6 + - - +
267B GLU* 1.3 81.6 - - - +
269B LEU* 1.3 63.7 + - - +
270B PHE 3.1 3.4 + - - -
271B GLN 3.7 7.5 + - - -
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Residues in contact with LEU 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271A GLN* 3.9 3.6 - - - +
65B PRO* 4.8 2.2 - - + -
69B PRO* 3.8 20.4 - - + -
222B TYR* 3.2 39.7 - - + +
223B SER 3.1 38.1 + - - +
224B PHE* 4.0 20.0 - - + -
245B PHE* 4.4 4.3 - - + -
261B TYR* 4.0 16.6 - - + -
265B LYS 4.0 0.6 + - - +
266B HIS* 2.9 42.6 + - + +
268B THR* 1.3 81.2 + - - +
270B PHE* 1.3 61.6 + - + +
271B GLN 3.4 1.8 + - - -
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Residues in contact with PHE 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265A LYS* 5.0 13.8 - - - +
268A THR* 3.7 15.4 - - + +
220B TYR* 4.8 2.7 - - + -
221B TYR* 3.2 37.7 + + + +
222B TYR* 4.0 8.3 - - + +
245B PHE* 3.8 26.7 - + - -
246B MET* 3.4 45.1 - - + -
266B HIS* 3.5 43.7 - + - -
267B GLU* 3.4 22.4 - - - +
268B THR 3.1 2.0 - - - -
269B LEU* 1.3 78.4 - - + +
271B GLN* 1.3 64.9 + - - +
272B MET* 3.4 7.9 + - - +
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Residues in contact with GLN 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223A SER* 3.3 27.3 + - - +
224A PHE* 3.5 23.4 - - + -
225A PRO* 3.4 26.4 - - + +
232A PRO* 6.0 0.9 - - - +
268A THR* 3.4 39.9 + - - +
269A LEU* 4.0 6.7 - - - +
271A GLN* 4.1 19.9 - - - +
223B SER* 2.6 34.8 + - - +
268B THR 3.7 5.3 + - - +
269B LEU 3.4 4.8 + - - -
270B PHE* 1.3 78.0 - - - +
272B MET* 1.3 67.9 - - - +
273B PRO* 4.9 0.8 - - + +
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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