Contacts of the helix formed by residues 281 - 289 (chain B) in PDB entry 2CXQ
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 281 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B MET* 4.1 6.7 - - - -
276B LEU* 3.2 23.5 + - - -
278B SER 2.9 10.2 + - - -
280B ILE* 1.3 76.0 - - - +
282B LEU* 1.3 62.7 + - - +
283B SER 3.2 2.5 - - - -
284B ILE* 2.9 30.7 + - - +
285B ALA* 3.1 10.6 + - - +
293B PHE* 3.8 6.1 - - - -
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Residues in contact with LEU 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B MET* 3.8 38.6 - - + +
132B PHE* 3.9 28.7 - - + -
133B CYS* 4.2 11.2 - - - -
207B ILE* 4.3 10.8 - - + -
244B VAL* 4.4 3.6 - - + -
246B LEU* 3.7 26.0 - - + -
264B PHE* 3.8 22.2 - - + -
279B ALA 2.9 18.2 + - - +
280B ILE 3.1 2.2 - - - -
281B GLY* 1.3 76.1 - - - +
283B SER* 1.3 58.3 + - - +
285B ALA* 3.2 2.0 + - - +
286B LEU* 2.9 34.5 + - + +
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Residues in contact with SER 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B ILE* 4.6 1.7 - - - +
154B ASN* 4.0 13.2 + - - -
164B PRO* 3.3 26.3 - - - +
168B THR* 4.0 3.4 - - - +
181B VAL* 4.1 22.0 - - - +
183B PHE* 3.6 9.2 - - - -
207B ILE* 4.1 21.5 - - - +
246B LEU* 5.4 0.2 - - - +
280B ILE 4.4 1.3 + - - -
282B LEU* 1.3 78.4 - - - +
284B ILE* 1.3 63.8 + - - +
286B LEU* 3.9 5.3 - - - +
287B HIS* 3.1 24.9 + - - +
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Residues in contact with ILE 284 (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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164B PRO* 3.8 27.8 - - + -
167B VAL* 3.8 43.1 - - + -
168B THR* 3.8 13.9 - - + -
171B LEU* 5.0 1.8 - - + -
276B LEU* 4.2 18.4 - - + +
281B GLY* 2.9 22.4 + - - +
283B SER* 1.3 77.3 + - - +
285B ALA* 1.3 58.2 + - - +
287B HIS* 3.1 2.4 + - - +
288B VAL* 2.9 48.6 + - + +
293B PHE* 3.9 18.6 - - + -
296B LEU* 4.4 3.6 - - + -
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Residues in contact with ALA 285 (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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129B MET* 4.8 4.0 - - + -
133B CYS* 3.6 20.9 - - - -
137B ARG* 4.1 0.7 - - - -
281B GLY 3.1 5.6 + - - +
282B LEU* 3.7 8.5 - - - +
284B ILE* 1.3 79.1 - - - +
286B LEU* 1.3 57.9 + - - +
289B GLY* 2.7 41.3 + - - -
290B PHE* 3.6 12.8 + - + -
293B PHE* 3.8 28.0 - - + -
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Residues in contact with LEU 286 (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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132B PHE* 3.9 21.5 - - + -
133B CYS* 3.9 25.8 - - - +
136B VAL* 3.7 31.0 - - + -
137B ARG* 2.9 28.6 + - + +
152B ILE* 3.4 31.4 - - + -
179B PRO* 3.4 11.7 - - - +
205B LEU* 5.4 0.4 - - + -
207B ILE* 3.6 28.0 - - + -
282B LEU* 2.9 22.5 + - + +
283B SER* 3.9 4.3 - - - +
285B ALA* 1.3 78.3 - - - +
287B HIS* 1.3 57.0 + - - +
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Residues in contact with HIS 287 (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 ARG* 3.1 11.4 + - - -
168B THR* 3.9 31.4 - - + -
172B LYS* 3.0 31.4 + - + +
175B SER* 3.3 48.2 - - - -
178B GLY* 3.6 6.2 - - - -
179B PRO* 2.9 31.3 + - - -
180B ARG* 4.5 3.1 - - - -
181B VAL* 3.6 20.2 - - + +
283B SER 3.1 19.4 + - - +
284B ILE 3.1 3.1 + - - +
286B LEU* 1.3 78.0 - - - +
288B VAL* 1.3 64.4 + - + +
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Residues in contact with VAL 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B ARG* 3.7 6.9 + - - -
168B THR* 5.6 2.0 - - - +
171B LEU* 3.5 40.2 - - + +
174B TYR* 3.4 24.0 - - + +
175B SER* 4.1 5.2 - - - +
284B ILE* 2.9 36.5 + - + +
287B HIS* 1.3 87.1 - - + +
289B GLY* 1.3 64.0 + - - +
292B HIS* 2.8 48.1 + - + -
293B PHE 4.5 2.7 - - - +
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Residues in contact with GLY 289 (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 ARG* 3.2 25.5 - - - +
285B ALA 2.7 23.5 + - - +
288B VAL* 1.3 79.1 - - - +
290B PHE* 1.3 64.4 + - - -
291B ASP* 3.3 3.1 - - - -
292B HIS 3.3 2.2 + - - -
293B PHE* 3.1 18.5 + - - +
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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