Contacts of the helix formed by residues 253 - 267 (chain B) in PDB entry 4CZ8
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 253 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160B PRO 4.3 7.4 + - - -
163B ILE* 5.3 0.2 - - - +
164B VAL* 4.2 17.9 + - - +
167B LEU* 6.2 4.5 - - - -
202B ASN* 3.1 26.2 + - - +
206B SER* 3.5 1.9 + - - -
248B GLU* 4.1 3.6 - - - -
252B ALA* 1.3 68.3 - - - +
254B GLY* 1.3 62.6 + - - +
255B TYR* 3.6 15.8 + - - +
256B LEU* 3.1 27.8 + - - +
257B VAL* 3.1 23.4 + - - +
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Residues in contact with GLY 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B GLY 4.2 0.4 - - - -
244B PHE* 3.4 43.4 - - - -
248B GLU* 3.1 9.0 + - - -
252B ALA 2.9 9.7 + - - -
253B SER* 1.3 68.8 - - - +
255B TYR* 1.3 59.9 + - - +
257B VAL* 3.3 8.5 + - - +
258B ALA* 2.9 31.4 + - - +
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Residues in contact with TYR 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B ARG* 5.1 2.9 - - - +
63B VAL* 3.4 29.3 - - - +
66B LEU* 3.7 37.0 - - + +
67B VAL* 3.7 29.8 - - + +
70B LEU* 3.7 17.2 - - + +
160B PRO* 4.2 2.5 - - + -
163B ILE* 3.9 33.4 - - + -
167B LEU* 5.4 8.5 - - + -
244B PHE* 3.6 17.5 - + - -
248B GLU* 4.5 9.0 - - - -
253B SER* 3.7 11.4 - - - +
254B GLY* 1.3 80.3 - - - +
256B LEU* 1.3 53.2 + - - +
258B ALA* 3.6 5.6 - - - +
259B THR* 2.6 37.4 + - - -
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Residues in contact with LEU 256 (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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157B PHE* 5.1 9.4 - - + +
160B PRO* 3.6 32.0 - - + +
161B LEU* 4.1 24.5 - - + -
164B VAL* 5.8 1.1 - - + -
202B ASN* 4.8 4.3 - - - +
203B VAL* 4.3 18.6 - - + +
206B SER* 3.6 24.0 - - - +
207B ILE* 4.4 12.6 - - + -
253B SER* 3.1 19.6 + - - +
255B TYR* 1.3 77.8 - - - +
257B VAL* 1.3 64.5 + - - +
259B THR* 3.2 6.0 + - + -
260B VAL* 2.9 40.3 + - + +
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Residues in contact with VAL 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B SER* 3.5 33.4 - - - +
209B LEU* 4.3 12.1 - - + -
210B GLY* 3.7 17.6 - - - +
213B LEU* 4.6 1.3 - - + -
243B GLY* 3.4 33.9 - - - +
247B GLY* 4.3 10.3 - - - -
252B ALA* 5.1 0.7 - - + -
253B SER 3.1 18.0 + - - +
254B GLY* 3.4 8.7 - - - +
256B LEU* 1.3 75.0 - - - +
258B ALA* 1.3 57.5 + - - +
260B VAL* 3.1 5.4 + - - +
261B THR* 2.9 31.8 + - - +
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Residues in contact with ALA 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B VAL* 4.3 21.1 - - + +
71B PHE* 3.1 27.7 - - + -
240B ALA* 3.9 21.8 - - - +
243B GLY* 5.5 0.2 - - - -
244B PHE 4.9 0.2 - - - +
254B GLY 2.9 17.4 + - - +
255B TYR* 3.6 5.2 - - - +
257B VAL* 1.3 77.7 - - - +
259B THR* 1.3 57.9 + - - +
261B THR* 3.2 8.1 + - - -
262B GLY 2.9 23.4 + - - -
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Residues in contact with THR 259 (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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70B LEU* 3.3 40.4 - - + +
71B PHE* 4.4 0.6 - - - +
73B GLU* 5.1 1.3 - - + +
74B GLY* 3.5 9.8 - - - +
156B ILE* 3.9 26.7 - - + +
157B PHE* 5.9 0.9 - - + -
160B PRO* 4.0 11.1 - - + +
255B TYR 2.6 22.8 + - - -
256B LEU* 3.2 13.1 + - + -
258B ALA* 1.3 75.9 - - - +
260B VAL* 1.3 57.3 + - - +
262B GLY* 3.0 4.7 + - - -
263B ILE* 2.9 34.7 + - + +
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Residues in contact with VAL 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B PHE* 5.7 0.7 - - + -
206B SER 4.5 0.9 - - - +
207B ILE* 3.6 38.1 - - + +
210B GLY* 3.7 2.9 - - - -
211B ILE* 3.3 44.9 - - + +
256B LEU* 2.9 27.4 + - + +
257B VAL 3.4 7.2 - - - +
259B THR* 1.3 74.5 - - - +
261B THR* 1.3 57.8 + - - +
263B ILE* 3.0 21.8 + - + +
264B VAL* 2.9 27.0 + - + +
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Residues in contact with THR 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B PHE* 4.0 13.0 - - + -
210B GLY* 3.5 18.2 + - - -
213B LEU* 4.5 4.5 - - + +
214B GLY* 3.7 20.7 + - - +
239B LEU* 3.8 29.9 + - + +
240B ALA* 5.5 1.2 - - - -
243B GLY* 5.3 2.6 - - - -
257B VAL* 2.9 20.1 + - - +
258B ALA* 3.4 10.8 - - - -
260B VAL* 1.3 75.3 - - - +
262B GLY* 1.3 57.6 + - - +
264B VAL* 3.1 5.7 + - - +
265B LEU* 2.9 31.1 + - + +
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Residues in contact with GLY 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B PHE* 3.7 16.0 - - - -
74B GLY 3.3 7.0 - - - -
75B HIS* 2.6 41.7 + - - -
258B ALA 2.9 12.0 + - - -
259B THR 3.0 5.1 + - - -
261B THR* 1.3 77.6 - - - +
263B ILE* 1.3 55.0 + - - +
266B GLY 2.9 14.9 + - - -
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Residues in contact with ILE 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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74B GLY* 3.1 19.3 - - - +
77B LEU* 3.7 34.5 - - + -
79B TRP* 5.4 11.2 - - + +
82B LEU* 6.1 1.6 - - + -
156B ILE* 5.2 2.0 - - + -
157B PHE* 4.1 20.4 - - + -
259B THR* 2.9 18.1 + - + +
260B VAL* 3.0 26.7 + - + +
262B GLY* 1.3 73.5 - - - +
264B VAL* 1.3 61.0 + - + +
266B GLY 3.2 0.9 + - - -
267B ASN* 2.3 50.4 + - - +
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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
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210B GLY 4.2 3.1 - - - +
211B ILE* 3.9 35.9 - - + +
214B GLY* 3.4 29.6 - - - +
215B ILE* 3.5 6.3 - - + +
218B TYR* 5.3 1.1 - - + -
260B VAL* 2.9 19.6 + - + +
261B THR 3.4 7.4 - - - +
263B ILE* 1.3 76.1 - - + +
265B LEU* 1.3 60.5 + - + +
267B ASN* 2.9 30.8 + - - +
268B TYR* 3.2 3.1 + - - -
271B LEU* 3.8 20.6 - - + -
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Residues in contact with LEU 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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71B PHE* 4.1 24.7 - - + -
75B HIS* 3.8 14.8 - - + -
214B GLY* 4.0 20.4 - - - +
218B TYR* 4.3 23.3 - - + +
221B ILE* 5.0 13.5 - - + -
236B SER* 5.0 8.3 - - - -
239B LEU* 4.3 17.7 - - + -
261B THR* 2.9 20.1 + - + +
264B VAL* 1.3 77.5 - - - +
266B GLY* 1.3 61.2 + - - +
268B TYR* 3.2 25.9 - - + +
287B ILE* 4.3 24.3 - - + +
290B GLU* 4.8 4.5 - - - +
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Residues in contact with GLY 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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75B HIS* 3.7 24.6 + - - -
262B GLY 2.9 16.3 + - - -
263B ILE 3.6 3.8 - - - -
264B VAL 3.2 0.4 - - - -
265B LEU* 1.3 77.5 - - - +
267B ASN* 1.3 61.5 + - - +
268B TYR* 3.5 9.2 + - - -
287B ILE* 5.7 3.4 - - - -
1423B FLC 2.8 27.7 + - - +
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Residues in contact with ASN 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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77B LEU 2.9 20.8 + - - -
78B SER* 3.4 7.1 - - - -
79B TRP* 2.6 37.3 + - + +
263B ILE* 2.3 46.6 + - - +
264B VAL* 3.1 7.0 - - - +
266B GLY* 1.3 77.6 - - - +
268B TYR* 1.3 61.3 + - - +
269B LYS 3.2 3.4 - - - +
270B LEU* 3.3 35.7 + - + +
271B LEU* 3.3 14.6 - - + +
1423B FLC 3.8 4.1 - - - +
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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