Contacts of the helix formed by residues 258 - 273 (chain B) in PDB entry 5CRX
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 THR 258 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174B ILE* 3.9 16.1 - - + +
175B ALA* 3.8 37.0 - - + +
178B ALA* 4.7 8.1 - - + -
255B GLN* 5.2 6.3 - - - +
256B LEU 3.5 0.8 + - - +
257B SER* 1.3 69.3 + - - +
259B ARG* 1.3 67.5 + - - +
260B ALA 3.0 0.2 - - - -
261B LEU* 3.2 12.6 + - - +
262B GLU* 3.0 30.6 + - - +
25D T 4.9 4.1 + - - +
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Residues in contact with ARG 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B SER* 2.9 13.9 - - - +
258B THR* 1.3 84.0 + - - +
260B ALA* 1.3 58.2 + - - +
262B GLU* 3.5 20.3 + - - +
263B GLY* 3.1 16.5 + - - +
7C T 4.2 10.5 - - + -
8C T 3.7 26.0 - - + +
9C C 4.0 6.1 - - - +
27D C 3.9 27.6 - - - +
28D G 2.5 57.9 + - - -
29D A 4.0 8.0 - - - +
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Residues in contact with ALA 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B LEU* 3.6 18.2 - - + -
257B SER* 2.7 18.2 + - - +
259B ARG* 1.3 76.9 - - - +
261B LEU* 1.3 55.7 + - - +
263B GLY* 2.6 22.5 + - - +
264B ILE* 2.8 16.7 + - + +
6C C 4.3 15.3 - - - +
7C T 3.4 25.8 - - + +
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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
----------------------------------------------------------
163B PHE* 3.5 37.1 - - + -
174B ILE* 3.5 39.5 - - + +
177B ILE* 4.7 1.6 - - + -
178B ALA* 3.8 22.7 - - + +
239B PHE* 5.1 9.4 - - + -
256B LEU* 3.8 21.3 - - + +
257B SER 3.1 10.3 + - - +
258B THR* 3.2 10.7 + - - +
260B ALA* 1.3 75.4 - - - +
262B GLU* 1.3 62.3 + - - +
264B ILE* 2.9 37.7 + - + +
265B PHE* 3.3 6.0 + - - -
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Residues in contact with GLU 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B ILE* 3.6 14.1 - - + -
258B THR* 3.0 21.6 + - - +
259B ARG* 3.5 26.6 - - - +
261B LEU* 1.3 76.2 - - - +
263B GLY* 1.3 61.2 + - - +
265B PHE* 3.3 5.8 + - - +
266B GLU* 3.2 20.1 + - - +
286B TRP 4.2 2.8 - - - +
287B SER* 4.6 3.1 - - - -
288B GLY* 3.8 12.3 - - - +
25D T 3.6 2.6 - - - +
26D A 2.5 67.0 + - + +
27D C 4.0 15.2 + - - +
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Residues in contact with GLY 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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259B ARG* 3.1 14.4 + - - -
260B ALA* 2.6 12.2 + - - -
262B GLU* 1.3 76.9 - - - +
264B ILE* 1.3 65.6 + - - -
266B GLU* 3.2 6.8 + - - +
267B ALA* 3.1 24.6 + - - +
270B ARG* 5.4 0.2 + - - -
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Residues in contact with ILE 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B ARG* 4.6 15.7 - - - +
160B ASN* 3.4 38.3 + - + +
163B PHE* 3.3 27.6 - - + -
164B LEU* 3.9 24.5 - - + -
256B LEU* 4.8 2.7 - - + -
260B ALA* 2.8 28.5 + - + +
261B LEU* 2.9 33.2 + - + +
263B GLY* 1.3 74.9 - - - +
265B PHE* 1.3 59.1 + - - +
267B ALA* 3.7 3.4 - - - +
268B THR* 3.0 28.8 + - - +
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Residues in contact with PHE 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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137B PHE* 4.1 21.3 - + - -
163B PHE* 3.8 29.6 - + - -
164B LEU* 3.5 26.7 - - + -
167B ALA* 4.2 8.1 - - + -
174B ILE* 4.8 0.2 - - + -
261B LEU 3.3 4.9 + - - -
262B GLU 3.4 7.6 - - - +
263B GLY 3.1 0.6 - - - -
264B ILE* 1.3 81.8 - - - +
266B GLU* 1.3 59.3 + - - +
268B THR* 4.8 1.8 - - - -
269B HIS* 3.3 12.9 + - - +
286B TRP* 3.2 53.0 - + + +
287B SER* 3.2 25.6 - - - +
288B GLY* 3.7 16.4 - - - -
290B SER* 4.3 4.9 - - - -
291B ALA* 3.8 24.7 - - + -
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Residues in contact with GLU 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 GLU 3.2 12.0 + - - +
263B GLY* 3.2 11.0 + - - +
265B PHE* 1.3 74.5 - - - +
267B ALA* 1.3 56.3 + - - +
269B HIS* 3.2 6.0 + - - +
270B ARG* 2.8 69.1 + - - +
276B LYS* 3.5 40.9 + - - +
285B ALA* 4.3 9.8 - - + +
286B TRP 3.6 6.9 + - - +
28D G 5.1 4.3 + - - -
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Residues in contact with ALA 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B ASN* 5.4 6.7 - - - +
263B GLY 3.1 16.7 + - - +
264B ILE* 3.7 5.2 - - - +
266B GLU* 1.3 72.2 - - - +
268B THR* 1.3 57.1 + - - +
269B HIS 3.0 1.1 - - - -
270B ARG* 3.0 31.2 + - - +
271B LEU* 2.8 36.4 + - - +
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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
----------------------------------------------------------
137B PHE* 4.5 2.9 - - + -
145B VAL* 3.3 42.5 - - + +
149B MET* 4.8 8.6 - - - +
160B ASN* 4.9 5.4 + - - +
164B LEU* 3.5 23.3 - - + +
264B ILE* 3.0 17.3 + - - +
265B PHE* 4.4 5.6 - - - -
267B ALA* 1.3 77.4 - - - +
269B HIS* 1.3 62.3 + - - +
271B LEU* 3.5 11.1 + - + +
272B ILE* 3.3 23.4 + - + +
286B TRP* 3.8 9.2 - - + -
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Residues in contact with HIS 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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135B LEU* 4.3 9.2 - - + +
265B PHE 3.3 13.8 + - - +
266B GLU* 3.2 5.3 + - - +
267B ALA 3.0 0.4 - - - -
268B THR* 1.3 76.6 - - - +
270B ARG* 1.3 61.1 + - - +
271B LEU 3.0 2.0 - - - -
272B ILE 3.1 1.4 + - - -
273B TYR* 2.6 70.3 + + + +
274B GLY 4.2 7.3 + - - -
276B LYS* 6.0 4.0 - - - -
284B LEU 3.7 22.4 + - - -
285B ALA* 3.7 14.0 - - + +
286B TRP* 3.3 48.7 - + + +
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Residues in contact with ARG 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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263B GLY 5.4 0.2 + - - -
266B GLU* 2.8 48.9 + - - +
267B ALA* 3.4 30.6 + - - +
269B HIS* 1.3 75.6 + - - +
271B LEU* 1.3 58.8 + - - +
274B GLY* 2.7 50.0 + - - +
275B ALA* 4.1 13.2 - - + +
276B LYS 5.4 0.9 - - - +
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Residues in contact with LEU 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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145B VAL* 5.6 0.7 - - + -
148B LEU* 4.3 11.9 - - + -
149B MET* 4.8 23.1 - - + -
267B ALA 2.8 15.6 + - - +
268B THR* 3.6 13.0 - - + +
270B ARG* 1.3 81.1 - - - +
272B ILE* 1.3 91.2 + - + +
274B GLY 4.4 0.9 + - - -
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Residues in contact with ILE 272 (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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144B GLN* 5.0 12.3 - - + +
145B VAL* 4.5 23.6 - - + +
148B LEU* 3.3 26.5 - - + -
268B THR 3.3 14.1 - - - +
269B HIS 3.1 2.0 + - - +
271B LEU* 1.3 101.5 - - + +
273B TYR* 1.3 96.2 + - + +
274B GLY 3.7 0.2 - - - -
286B TRP* 4.7 1.1 - - + -
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Residues in contact with TYR 273 (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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141B ASP* 3.8 12.9 + - - +
144B GLN* 3.7 17.7 + - - -
269B HIS* 2.6 48.1 + + + +
272B ILE* 1.3 102.0 - - + +
274B GLY* 1.3 61.5 + - - +
275B ALA 5.0 1.4 - - - +
286B TRP* 3.8 21.1 - + - -
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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
------------------------------------------------------------
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