Contacts of the helix formed by residues 249 - 261 (chain B) in PDB entry 2CUY
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 ARG 249 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155B LEU* 4.4 14.4 - - + -
224B ASN 3.3 16.9 + - - +
225B VAL 2.7 27.1 + - - -
226B THR* 3.1 26.4 + - - +
227B ALA* 3.9 10.3 - - + +
247B PRO* 4.1 9.9 - - + +
248B VAL* 1.3 68.7 - - - +
250B TRP* 1.3 63.7 + - - +
251B VAL 3.4 2.2 - - - -
252B GLU* 2.7 47.5 + - - +
253B ILE* 3.1 27.1 + - - +
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Residues in contact with TRP 250 (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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5B LEU* 4.0 21.3 - - + -
86B ALA* 3.9 28.9 - - + -
87B GLY 3.5 26.9 - - - -
88B HIS* 3.7 17.9 - + + -
155B LEU 3.2 10.4 + - - +
156B ASN* 3.7 28.3 - - - +
224B ASN* 4.2 5.2 - - - -
248B VAL* 3.0 8.8 + - + +
249B ARG* 1.3 72.3 - - - +
251B VAL* 1.3 66.2 + - - +
253B ILE* 3.0 28.7 + - + +
254B LEU* 3.0 42.6 + - + +
274B LEU* 3.7 42.3 + - + +
277B LEU* 3.8 18.1 - - + +
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Residues in contact with VAL 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B LEU* 2.8 33.9 + - + +
156B ASN 3.5 23.3 + - - +
157B ALA* 3.5 19.7 - - - +
158B PRO* 4.1 6.7 - - + -
249B ARG 3.4 0.4 - - - -
250B TRP* 1.3 72.4 - - - +
252B GLU* 1.3 66.6 + - + +
254B LEU* 3.3 3.9 + - - +
255B ARG* 3.0 49.3 + - + +
281B THR* 4.5 10.7 - - + +
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Residues in contact with GLU 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B LEU* 5.1 6.6 - - - +
227B ALA* 3.8 13.5 - - + +
228B ARG* 4.7 6.6 + - - +
249B ARG* 2.7 59.9 + - - +
250B TRP 3.2 0.6 - - - -
251B VAL* 1.3 81.3 - - + +
253B ILE* 1.3 65.3 + - - +
255B ARG* 3.2 9.4 + - + +
256B ASP* 2.9 24.3 + - - +
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Residues in contact with ILE 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B ALA* 4.0 7.2 - - + -
222B TYR* 3.7 27.2 - - + -
223B SER 3.9 11.0 - - - +
224B ASN* 3.3 32.3 - - - +
227B ALA* 3.8 18.8 - - - -
249B ARG 3.1 16.4 + - - +
250B TRP* 3.0 25.2 + - + +
252B GLU* 1.3 77.6 - - - +
254B LEU* 1.3 64.7 + - + +
256B ASP* 3.2 2.4 + - - +
257B MET* 3.0 49.1 + - + +
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Residues in contact with LEU 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B LEU* 4.5 3.1 - - + -
156B ASN 4.6 1.3 - - - +
250B TRP* 3.0 57.9 + - + +
251B VAL 3.3 5.6 + - - +
253B ILE* 1.3 75.9 - - + +
255B ARG* 1.3 63.8 + - - +
257B MET* 3.3 11.3 + - - +
258B GLU 3.0 18.2 + - - -
265B PHE* 4.3 13.5 - - + -
277B LEU 4.0 8.7 - - - +
278B VAL* 3.9 25.6 - - + -
281B THR* 3.8 31.0 - - + +
282B LEU* 3.3 22.1 - - + +
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Residues in contact with ARG 255 (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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158B PRO* 4.0 22.2 - - - +
251B VAL* 3.0 28.7 + - + +
252B GLU* 3.5 10.5 - - + +
254B LEU* 1.3 76.8 - - - +
256B ASP* 1.3 56.9 + - - +
258B GLU* 3.2 9.7 + - - +
259B ALA* 2.9 26.9 + - - +
281B THR* 3.5 32.7 + - - +
282B LEU* 3.7 13.5 - - - +
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Residues in contact with ASP 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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222B TYR* 2.6 31.7 + - + +
228B ARG* 3.6 36.5 + - - +
252B GLU 2.9 13.3 + - - +
253B ILE 3.6 7.4 - - - +
255B ARG* 1.3 76.0 - - - +
257B MET* 1.3 52.2 + - - +
259B ALA* 3.0 10.6 + - - +
260B ARG* 2.6 62.3 + - - -
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Residues in contact with MET 257 (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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3B ALA* 3.6 16.8 - - + -
5B LEU* 4.0 11.2 - - + -
84B LEU* 4.9 2.2 - - + -
85B ALA* 4.1 7.6 - - - +
86B ALA* 3.4 32.3 - - + -
222B TYR* 3.6 28.5 - - + +
253B ILE* 3.0 26.5 + - + +
254B LEU* 3.3 13.0 - - - +
256B ASP* 1.3 72.6 - - - +
258B GLU* 1.3 66.7 + - - +
260B ARG* 3.0 13.2 + - - +
261B GLY 3.1 0.3 + - - -
262B VAL* 3.0 31.7 + - + +
265B PHE* 3.5 31.6 - - + -
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Residues in contact with GLU 258 (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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254B LEU 3.0 13.1 + - - +
255B ARG* 3.2 10.9 - - - +
257B MET* 1.3 75.6 - - - +
259B ALA* 1.3 60.8 + - - +
261B GLY* 2.9 20.6 + - - -
262B VAL 3.8 16.7 + - - +
265B PHE* 4.8 0.8 - - - -
282B LEU* 4.0 30.5 - - + -
285B ALA* 5.9 3.4 - - + -
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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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255B ARG 2.9 13.6 + - - +
256B ASP* 3.0 17.5 + - - +
258B GLU* 1.3 76.9 + - - +
260B ARG* 1.3 61.5 + - - +
261B GLY* 3.0 6.6 + - - -
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Residues in contact with ARG 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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1B MET* 4.1 13.6 - - - +
84B LEU* 3.7 30.6 - - + +
222B TYR* 3.4 3.5 + - - -
228B ARG* 4.8 4.8 - - - +
229B PRO* 3.2 35.2 - - - +
256B ASP* 2.6 52.7 + - - +
257B MET 3.0 10.1 + - - +
259B ALA* 1.3 74.7 - - - +
261B GLY* 1.3 59.2 + - - +
262B VAL* 4.6 1.1 - - + -
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Residues in contact with GLY 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B MET* 3.3 17.5 - - - +
258B GLU 2.9 11.9 + - - -
259B ALA 3.0 2.5 - - - -
260B ARG* 1.3 81.0 - - - +
262B VAL* 1.3 64.0 + - - +
263B LYS* 3.5 7.6 + - - +
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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