Contacts of the helix formed by residues 161 - 171 (chain B) in PDB entry 2CXU
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 ASP 161 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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386A ASN* 5.9 1.2 - - - +
154B ASN* 4.4 4.3 + - - +
156B GLY 3.4 22.8 - - - +
157B ILE 4.2 2.9 - - - -
158B GLY 2.9 8.9 + - - +
159B GLY 3.2 0.6 - - - -
160B SER* 1.3 77.9 - - - +
162B LEU* 1.3 83.1 + - - +
163B GLY 3.3 2.0 + - - -
164B PRO* 3.4 5.2 - - - +
165B LEU* 3.0 32.9 + - - +
183B PHE* 3.7 24.6 - - - +
184B VAL 4.7 1.0 - - - +
185B SER* 3.5 27.7 + - - -
191B HIS* 5.8 0.2 - - - -
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Residues in contact with LEU 162 (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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386A ASN* 5.8 5.8 - - + +
390A ALA* 3.9 15.0 - - + -
158B GLY* 2.9 21.3 + - - +
159B GLY* 5.3 0.7 - - - -
161B ASP* 1.3 86.2 - - - +
163B GLY* 1.3 58.4 + - - +
165B LEU* 3.8 9.8 - - + +
166B MET* 2.8 32.9 + - - +
347B ARG* 5.5 4.6 - - - +
350B ALA* 3.8 30.3 - - + +
351B TYR* 3.7 16.7 - - + +
354B GLN* 3.4 38.8 - - + +
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Residues in contact with GLY 163 (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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159B GLY* 4.7 4.7 + - - -
162B LEU* 1.3 75.1 - - - +
164B PRO* 1.3 66.9 - - - +
166B MET* 3.3 1.4 + - - -
167B VAL* 2.9 37.8 + - - +
276B LEU* 3.8 14.1 - - - -
351B TYR* 3.4 25.7 - - - -
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Residues in contact with PRO 164 (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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154B ASN* 4.7 2.0 - - - +
159B GLY 4.3 6.7 - - - +
160B SER 4.1 9.2 - - - +
161B ASP* 3.4 15.5 - - - +
163B GLY* 1.3 89.3 - - - +
165B LEU* 1.3 55.7 + - - +
168B THR* 2.8 36.7 + - - +
183B PHE* 3.5 12.1 - - + -
276B LEU* 4.5 3.6 - - + -
280B ILE* 3.6 32.3 - - + +
281B GLY* 4.9 0.2 - - - -
283B SER* 3.3 23.3 - - - +
284B ILE* 3.8 16.1 - - + -
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Residues in contact with LEU 165 (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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161B ASP* 3.0 34.4 + - - +
162B LEU* 3.9 8.7 - - + +
164B PRO* 1.3 73.9 - - - +
166B MET* 1.3 66.5 + - - +
168B THR* 3.2 1.7 + - - -
169B GLU* 3.0 47.8 + - + +
183B PHE* 3.5 38.9 - - + -
346B HIS* 6.3 0.2 - - + -
347B ARG* 4.6 24.0 - - + +
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Residues in contact with MET 166 (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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162B LEU 2.8 22.4 + - - +
163B GLY 3.9 0.2 - - - +
165B LEU* 1.3 74.0 - - - +
167B VAL* 1.3 69.6 + - + +
169B GLU* 3.4 3.0 + - - +
170B ALA* 2.9 30.9 + - - +
344B TYR 4.6 0.9 - - - +
345B MET* 5.9 1.8 - - - -
347B ARG* 3.4 45.2 + - + +
348B PHE* 3.7 23.6 - - + +
351B TYR* 3.7 34.8 - - + -
487B LEU* 4.5 10.5 - - - -
491B ILE* 3.8 28.5 - - + -
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Residues in contact with VAL 167 (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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163B GLY 2.9 20.1 + - - +
166B MET* 1.3 81.7 - - - +
168B THR* 1.3 60.3 + - - +
170B ALA* 3.2 0.5 + - - -
171B LEU* 2.9 52.4 + - + +
276B LEU* 3.9 25.4 - - + -
284B ILE* 3.7 31.6 - - + -
296B LEU* 4.0 7.4 - - + -
487B LEU* 4.0 7.4 - - + -
491B ILE* 4.0 19.3 - - + -
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Residues in contact with THR 168 (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 2.8 25.4 + - - +
165B LEU 3.2 2.4 + - - -
167B VAL* 1.3 75.7 - - - +
169B GLU* 1.3 63.6 + - - +
171B LEU* 3.7 3.4 - - - -
172B LYS* 3.1 31.3 + - - -
181B VAL* 3.9 5.8 - - + +
183B PHE* 3.2 26.5 - - + -
283B SER 4.0 7.4 - - - +
284B ILE* 3.8 31.2 - - + +
287B HIS* 3.7 26.1 - - + -
288B VAL* 5.4 1.6 - - + -
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Residues in contact with GLU 169 (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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194A LYS* 4.5 12.5 + - - -
165B LEU* 3.0 42.3 + - + +
166B MET* 3.6 6.3 - - - +
168B THR* 1.3 79.2 + - - +
170B ALA* 1.3 60.4 + - - +
171B LEU 3.4 0.5 + - - -
172B LYS* 3.5 27.1 + - - +
183B PHE* 5.8 1.0 - - - -
344B TYR* 3.2 30.9 - - - +
346B HIS* 2.8 39.3 + - + +
347B ARG* 4.6 3.6 - - + -
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Residues in contact with ALA 170 (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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166B MET* 2.9 21.2 + - - +
167B VAL 3.2 0.4 + - - +
169B GLU* 1.3 77.1 - - - +
171B LEU* 1.3 64.6 + - - +
172B LYS 3.4 1.0 + - - -
173B PRO* 4.2 3.3 - - - +
344B TYR* 3.2 32.3 + - - +
345B MET* 4.7 4.0 - - + -
413B GLN* 6.0 0.5 - - - +
482B LEU* 4.0 23.1 - - + +
487B LEU* 3.8 28.3 - - + -
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Residues in contact with LEU 171 (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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167B VAL* 2.9 37.0 + - + +
168B THR 3.7 3.4 - - - +
170B ALA* 1.3 81.2 - - + +
172B LYS* 1.3 58.8 + - - +
173B PRO* 3.2 5.6 - - - -
174B TYR* 2.8 37.0 + - + +
284B ILE* 5.1 1.1 - - + -
288B VAL* 3.6 29.1 - - + +
292B HIS 5.5 0.4 - - - +
296B LEU* 4.4 6.5 - - + -
482B LEU* 4.2 6.1 - - + +
483B THR 3.8 6.3 - - - +
484B PRO* 3.7 46.2 - - + -
487B LEU* 3.7 20.0 - - + -
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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