Contacts of the helix formed by residues 260 - 268 (chain B) in PDB entry 4CDC
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 SER 260 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240B MET* 4.1 9.4 - - - +
259B LEU* 1.3 70.8 - - - +
261B PRO* 1.3 64.6 - - - +
262B GLN 3.4 1.4 + - - -
263B GLU* 3.0 26.0 + - - +
264B VAL* 3.9 5.0 + - - +
292B LEU* 5.2 1.2 - - - +
293B VAL* 2.8 29.9 + - - +
294B GLU 3.5 16.2 - - - -
295B GLU* 3.7 5.6 - - - +
298B PHE* 2.8 27.2 + - - +
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Residues in contact with PRO 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B ARG* 3.5 11.2 - - - +
236B SER* 3.0 28.6 + - - +
237B PHE* 3.7 46.4 - - + -
240B MET* 3.9 13.7 - - + -
259B LEU 3.1 12.5 - - - +
260B SER* 1.3 84.8 - - - +
262B GLN* 1.3 57.6 + - - +
264B VAL 3.3 1.9 + - - -
265B VAL* 3.0 26.3 + - - +
295B GLU* 3.4 13.9 - - - +
300B TYR* 4.3 6.1 - - + -
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Residues in contact with GLN 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B SER 3.2 0.4 - - - -
261B PRO* 1.3 78.3 - - + +
263B GLU* 1.3 60.3 + - - +
265B VAL* 3.9 10.0 - - - +
266B SER* 2.8 53.2 + - - -
298B PHE* 3.5 31.6 - - + +
299B PRO 3.5 19.3 - - - +
300B TYR* 3.3 16.5 - - - -
301B THR* 3.1 12.3 + - + +
302B GLY* 2.9 29.3 + - - -
303B THR 3.0 21.2 + - - -
305B SER* 3.4 5.0 + - - +
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Residues in contact with GLU 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B SER* 3.0 22.0 + - - +
261B PRO 3.3 0.4 - - - -
262B GLN* 1.3 75.2 - - - +
264B VAL* 1.3 61.8 + - - +
267B CYS* 2.8 41.5 + - - +
286B TYR* 2.4 43.4 + - - -
291B GLY 4.1 0.5 - - - +
292B LEU* 4.0 11.1 - - - +
293B VAL* 3.9 20.1 + - + +
298B PHE* 3.7 24.2 - - + -
309B MET* 4.1 14.2 - - + +
315B ARG* 2.8 22.0 + - - +
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Residues in contact with VAL 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B TYR* 3.9 15.4 + - + -
236B SER* 3.6 12.8 - - - +
240B MET* 4.4 2.0 - - + -
260B SER 4.3 5.6 - - - +
261B PRO 3.3 7.7 + - - +
262B GLN 3.1 0.4 - - - -
263B GLU* 1.3 78.6 - - - +
265B VAL* 1.3 64.8 + - - +
268B SER* 3.0 29.0 + - - +
271B ALA* 5.2 0.7 - - - +
273B GLY* 5.2 0.9 - - - -
282B ILE* 3.7 43.5 - - + -
286B TYR* 4.0 8.5 - - + -
292B LEU* 3.5 32.3 - - + -
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Residues in contact with VAL 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B CYS* 4.0 9.9 - - - -
233B SER* 3.8 28.9 - - - -
235B TYR* 4.2 11.0 - - - +
236B SER* 4.5 4.0 - - - -
261B PRO 3.0 17.6 + - - +
262B GLN* 3.1 13.9 + - - +
264B VAL* 1.3 75.4 - - - +
266B SER* 1.3 60.9 + - - +
268B SER 5.0 1.2 + - - +
273B GLY* 3.3 35.5 + - - +
274B CYS 3.9 4.3 - - - +
300B TYR* 4.8 3.6 - - + -
303B THR 3.8 21.8 - - - +
304B ASP* 4.0 6.5 - - - +
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Residues in contact with SER 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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262B GLN* 2.8 39.9 + - - -
265B VAL* 1.3 79.5 - - - +
267B CYS* 1.3 59.5 + - - +
298B PHE* 3.8 20.0 - - - -
304B ASP 5.7 0.9 - - - -
305B SER* 2.9 32.0 + - - +
306B PRO 4.1 4.3 - - - -
307B CYS* 3.8 10.9 + - - +
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Residues in contact with CYS 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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263B GLU* 2.8 34.3 + - - +
266B SER* 1.3 79.1 - - - +
268B SER* 1.3 62.1 + - - +
269B GLN* 3.4 12.6 + - - +
286B TYR* 3.8 4.3 + - - +
298B PHE* 4.0 6.3 - - - -
307B CYS* 2.1 49.8 - - - -
309B MET* 3.6 18.6 - - - -
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Residues in contact with SER 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B GLU 3.9 0.6 + - - -
264B VAL* 3.0 36.6 + - - +
265B VAL 5.4 1.0 - - - +
266B SER 3.9 0.4 - - - -
267B CYS* 1.3 74.9 - - - +
269B GLN* 1.3 57.4 + - - +
270B TYR* 3.2 12.7 + - - +
271B ALA* 3.2 22.3 + - - +
273B GLY 5.1 2.3 + - - -
282B ILE* 3.5 13.0 - - - +
286B TYR* 3.2 36.1 - - - -
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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