Contacts of the helix formed by residues 257 - 268 (chain B) in PDB entry 6E8Z
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 GLY 257 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200B CYS* 4.0 15.5 - - - -
204B LYS* 5.7 0.3 - - - +
232B LEU* 5.0 3.8 - - - -
235B MET* 5.2 4.0 - - - +
252B PHE* 3.4 17.9 - - - -
254B GLU 2.9 5.5 + - - -
256B CYS* 1.3 82.3 - - - +
258B VAL* 1.3 66.0 + - - -
259B ALA 3.2 1.2 + - - -
260B ASP 3.4 0.9 + - - -
261B LEU* 2.8 27.1 + - - +
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Residues in contact with VAL 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A ARG* 3.6 27.1 - - + -
232A LEU* 4.8 11.2 - - + -
253A LEU* 6.3 0.4 - - + -
258A VAL* 3.6 30.1 - - + -
262A ILE* 5.7 0.2 - - + -
232B LEU* 4.8 16.6 - - + +
252B PHE 2.8 15.5 + - - +
253B LEU* 3.7 17.3 - - + +
254B GLU 3.3 1.0 + - - +
257B GLY* 1.3 74.4 - - - +
259B ALA* 1.3 61.2 + - - +
261B LEU* 3.4 6.1 + - + +
262B ILE* 2.9 51.0 + - + +
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Residues in contact with ALA 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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225A ALA* 3.9 17.3 - - + +
226A ALA* 5.4 0.2 - - - -
229A ARG* 4.0 12.6 - - + -
150B ALA* 3.8 15.2 - - + +
163B GLU* 4.7 1.8 - - - +
254B GLU 3.9 0.4 + - - -
255B SER* 3.4 25.2 + - - +
257B GLY 3.3 0.6 - - - -
258B VAL* 1.3 83.6 - - - +
260B ASP* 1.3 58.2 + - - +
262B ILE* 3.2 11.5 + - - +
263B THR* 2.8 31.9 + - - +
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Residues in contact with ASP 260 (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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120B LYS* 2.6 39.6 + - - +
148B MET* 5.7 0.7 - - - +
149B GLY* 3.4 10.6 + - - +
150B ALA* 3.8 7.1 - - - +
151B ASN 5.0 0.3 + - - -
201B GLY* 5.1 2.6 - - - -
204B LYS* 3.4 19.6 + - + +
255B SER 2.9 17.5 + - - +
256B CYS* 3.8 15.5 - - - +
257B GLY 3.4 0.2 + - - -
259B ALA* 1.3 71.3 - - - +
261B LEU* 1.3 65.4 + - - +
263B THR* 3.7 13.9 - - - +
264B THR* 2.7 36.7 + - - -
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Residues in contact with LEU 261 (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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204B LYS* 4.0 26.6 - - + +
207B VAL* 3.7 28.0 - - + -
228B ILE* 3.6 38.6 - - + +
232B LEU* 3.9 32.1 - - + +
235B MET* 4.1 7.0 - - - -
257B GLY 2.8 19.2 + - - +
258B VAL* 3.7 7.6 - - + +
260B ASP* 1.3 77.8 - - - +
262B ILE* 1.3 58.0 + - + +
264B THR* 3.2 2.8 + - - -
265B CYS* 2.8 43.6 + - - -
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Residues in contact with ILE 262 (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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225A ALA* 4.1 17.5 - - + +
228A ILE* 4.1 25.6 - - + -
229A ARG* 5.4 1.1 - - + +
262A ILE* 4.0 34.8 - - + -
266A TYR* 3.9 19.7 + - - +
228B ILE* 4.6 9.9 - - + -
258B VAL* 2.9 36.5 + - + +
259B ALA* 3.2 13.2 - - - +
261B LEU* 1.3 74.2 - - + +
263B THR* 1.3 67.4 + - - +
265B CYS* 4.7 1.6 - - - -
266B TYR* 3.1 39.5 + - + +
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Residues in contact with THR 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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221A ASP* 3.5 25.5 - - - +
222A ASN* 3.0 28.0 + - - +
225A ALA* 4.3 11.9 - - - -
266A TYR* 5.0 2.2 - - - -
150B ALA* 3.9 2.9 - - + -
259B ALA 2.8 16.2 + - - +
260B ASP* 3.4 26.0 - - - +
262B ILE* 1.3 78.5 - - - +
264B THR* 1.3 62.8 + - - +
266B TYR* 4.5 1.5 - - - +
267B GLY* 3.0 27.7 + - - -
268B GLY 3.9 0.7 + - - -
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Residues in contact with THR 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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204B LYS* 2.9 36.3 + - + +
205B ASN* 3.8 9.2 - - - +
208B ALA* 3.6 24.0 - - + +
260B ASP* 2.7 26.5 + - - -
261B LEU* 3.7 3.1 - - - -
263B THR* 1.3 81.7 - - - +
265B CYS* 1.3 59.4 + - - +
268B GLY* 2.9 35.3 + - - +
270B ASN* 5.3 5.2 - - + +
271B ARG* 4.1 2.3 - - - +
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Residues in contact with CYS 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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204B LYS 4.8 0.2 - - - -
207B VAL* 4.0 3.8 - - - -
208B ALA* 3.7 28.7 - - - -
211B ALA* 3.7 8.6 - - + +
224B LYS* 3.2 12.6 + - - -
228B ILE* 3.7 36.1 - - + -
261B LEU* 2.8 40.9 + - - +
262B ILE* 4.3 2.7 - - - +
264B THR* 1.3 77.1 - - - +
266B TYR* 1.3 59.0 + - + +
271B ARG* 3.1 22.2 - - - +
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Residues in contact with TYR 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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221A ASP* 4.5 8.4 - - - +
262A ILE* 4.0 21.8 + - + +
263A THR* 5.0 0.9 + - - -
266A TYR* 3.8 55.6 - + + -
221B ASP* 3.9 23.1 + - - -
224B LYS* 3.8 24.7 + - + +
225B ALA* 4.7 5.2 + - - +
228B ILE* 3.5 28.7 - - + +
262B ILE* 3.1 34.3 + - + +
263B THR 4.5 0.7 - - - +
265B CYS* 1.3 81.9 - - - +
267B GLY* 1.3 57.3 + - - +
268B GLY 3.8 0.4 - - - -
271B ARG* 3.9 12.8 + - - -
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Residues in contact with GLY 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A ASP* 4.5 14.7 + - - -
263B THR 3.0 14.7 + - - -
266B TYR* 1.3 76.7 - - - +
268B GLY* 1.3 64.1 + - - +
269B ARG 4.1 0.2 + - - -
271B ARG* 4.8 2.2 - - - -
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Residues in contact with GLY 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B THR* 2.9 31.9 + - - -
266B TYR 3.8 0.4 - - - -
267B GLY* 1.3 81.6 - - - +
269B ARG* 1.3 65.5 + - - -
270B ASN 3.4 2.5 - - - -
271B ARG* 3.3 8.1 + - - +
272B LYS* 3.2 19.6 + - - +
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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