Contacts of the helix formed by residues 249 - 260 (chain B) in PDB entry 2QJ3
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
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Residue Dist Surf HB Arom Phob DC
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156B ARG* 3.3 54.2 - - + +
224B ASN 2.9 19.5 + - - +
225B ARG 3.6 17.9 - - - +
227B GLY 4.5 0.7 + - - -
247B PRO* 4.2 15.5 - - + +
248B VAL* 1.3 74.3 - - - +
250B TRP* 1.3 64.6 + - - +
251B ASP* 3.1 35.6 + - - +
252B LEU* 3.1 43.3 + - + +
253B CYS* 3.3 15.2 + - - -
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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* 3.9 20.1 - - + +
88B ALA* 3.6 38.1 - - + -
89B GLY 3.0 31.2 - - - -
90B HIS* 3.8 27.6 - - + +
156B ARG 3.2 9.3 + - - +
157B ASN* 3.7 22.7 - - - -
224B ASN* 3.9 8.1 - - - -
248B VAL* 3.5 3.8 - - + +
249B ARG* 1.3 73.1 - - - +
251B ASP* 1.3 53.8 + - - +
253B CYS* 2.9 15.6 + - + +
254B THR* 2.7 48.0 + - - -
257B LEU* 5.6 3.1 - - + -
274B LEU* 3.6 41.3 + - + +
277B ILE* 4.3 17.6 - - + +
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Residues in contact with ASP 251 (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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139B GLU* 4.9 5.4 - - - +
156B ARG* 2.9 27.3 + - + +
157B ASN 3.7 13.9 + - - +
158B ALA* 4.7 4.9 - - - +
249B ARG* 3.2 45.4 + - - +
250B TRP* 1.3 76.2 - - - +
252B LEU* 1.3 73.6 + - - +
254B THR* 3.4 7.7 + - - -
255B ALA* 2.9 25.1 + - - +
258B ARG* 5.2 1.4 + - - -
281B GLU* 4.7 8.0 - - - +
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Residues in contact with LEU 252 (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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226B ASP* 3.4 37.2 - - + +
227B GLY* 3.7 2.1 - - - +
249B ARG* 3.1 46.6 + - + +
251B ASP* 1.3 91.3 + - - +
253B CYS* 1.3 61.1 + - - +
255B ALA* 3.5 12.1 - - + +
256B THR* 3.0 31.2 + - - -
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Residues in contact with CYS 253 (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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88B ALA* 4.7 4.5 - - + -
89B GLY 5.4 0.2 - - - -
222B LEU* 3.6 22.7 - - + +
223B SER 3.8 13.2 - - - -
224B ASN* 4.2 8.7 - - - -
227B GLY* 3.7 16.4 - - - -
249B ARG 3.5 13.9 - - - -
250B TRP* 2.9 36.9 + - + +
252B LEU* 1.3 74.0 - - - +
254B THR* 1.3 60.5 + - - +
256B THR* 3.2 3.6 + - - -
257B LEU* 2.9 35.9 + - + +
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Residues in contact with THR 254 (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 ASN 4.4 2.6 + - - -
250B TRP* 2.7 37.6 + - - -
251B ASP* 3.5 10.1 - - - -
253B CYS* 1.3 74.4 - - - +
255B ALA* 1.3 61.1 + - - +
257B LEU* 3.3 11.3 + - + +
258B ARG* 3.0 28.1 + - - +
277B ILE* 4.9 3.3 - - + +
278B ALA* 5.8 2.5 - - - -
281B GLU* 3.6 36.9 + - + +
282B LEU* 3.8 21.6 - - + +
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Residues in contact with ALA 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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251B ASP 2.9 14.2 + - - +
252B LEU* 3.5 20.0 - - + +
253B CYS 3.2 0.4 - - - -
254B THR* 1.3 75.7 - - - +
256B THR* 1.3 62.6 + - - +
258B ARG* 3.3 23.0 + - - +
259B GLU* 3.1 25.9 + - - +
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Residues in contact with THR 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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86B ILE* 4.5 1.3 - - + -
222B LEU* 3.7 25.8 - - + -
227B GLY 2.5 25.7 + - - +
228B LYS* 4.7 6.7 + - + +
229B PRO* 4.7 5.4 - - + -
252B LEU 3.0 8.6 + - - -
253B CYS 3.6 7.0 - - - -
255B ALA* 1.3 75.0 - - - +
257B LEU* 1.3 53.1 + - - +
259B GLU* 2.9 19.8 + - - +
260B HIS* 2.8 65.0 + - + +
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Residues in contact with LEU 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* 4.0 13.7 - - + -
5B LEU* 4.1 26.7 - - + -
86B ILE* 3.7 43.5 - - + -
88B ALA* 5.2 5.8 - - + -
222B LEU* 4.4 4.9 - - + -
250B TRP* 5.6 3.6 - - + -
253B CYS* 2.9 19.2 + - + +
254B THR* 3.4 17.3 - - + +
256B THR* 1.3 76.6 - - - +
258B ARG* 1.3 63.5 + - - +
260B HIS* 3.2 13.0 + - + +
262B VAL* 3.5 26.6 + - + +
265B ILE* 5.7 1.8 - - + -
282B LEU* 4.1 19.3 - - + -
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Residues in contact with ARG 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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251B ASP 5.2 1.0 + - - -
254B THR* 3.0 13.9 + - - +
255B ALA* 3.4 32.0 + - - +
257B LEU* 1.3 75.0 - - - +
259B GLU* 1.3 57.9 + - - +
261B THR* 3.0 21.5 + - - +
262B VAL* 5.1 2.5 - - - +
281B GLU* 2.6 37.2 + - - +
282B LEU* 3.7 20.4 - - + +
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Residues in contact with GLU 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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228B LYS* 4.6 12.6 + - - -
255B ALA* 3.1 11.0 + - - +
256B THR* 2.9 31.2 + - + +
258B ARG* 1.3 78.4 - - + +
260B HIS* 1.3 64.8 + - + +
261B THR* 3.3 6.0 + - - -
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Residues in contact with HIS 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 SER* 4.2 1.0 + - - -
1B MET* 3.4 32.3 - - + +
86B ILE* 4.0 23.2 - - + +
220B THR* 4.5 14.1 + - + +
222B LEU* 5.4 0.4 - - + -
229B PRO* 5.6 6.8 - - + +
256B THR* 2.8 47.0 + - + +
257B LEU* 3.7 6.7 - - - +
258B ARG 3.1 0.6 - - - -
259B GLU* 1.3 82.4 - - + +
261B THR* 1.3 71.6 + - - +
262B VAL* 3.3 1.2 + - + -
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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