Contacts of the helix formed by residues 181 - 193 (chain B) in PDB entry 1X1O
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 181 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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176B VAL* 2.9 19.3 + - - -
179B ALA* 4.0 0.9 - - - +
180B GLY* 1.3 81.5 - - - +
182B VAL* 1.3 65.9 + - - -
183B GLY 3.3 2.7 - - - -
184B GLU* 3.3 4.7 + - - +
185B ALA* 3.0 24.1 + - - +
211B GLU* 4.7 3.1 - - - -
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Residues in contact with VAL 182 (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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176B VAL* 3.5 25.0 - - + +
181B GLY* 1.3 71.0 - - - -
183B GLY* 1.3 58.4 + - - +
185B ALA* 3.3 1.3 + - - +
186B VAL* 2.9 41.7 + - + +
201B VAL* 4.2 7.9 - - + -
202B GLU 4.6 1.6 - - - +
203B VAL* 4.4 5.8 - - + -
208B GLU* 3.7 43.1 - - + +
211B GLU* 3.3 14.1 + - + +
212B ALA* 3.7 37.2 - - + +
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Residues in contact with GLY 183 (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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181B GLY* 3.3 0.8 - - - -
182B VAL* 1.3 78.2 - - - +
184B GLU* 1.3 55.1 - - - +
186B VAL* 3.3 1.7 + - - +
187B ARG* 3.0 53.6 + - - +
211B GLU* 3.0 19.4 + - - -
215B ALA* 3.9 14.8 - - - +
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Residues in contact with GLU 184 (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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179B ALA 2.9 28.7 - - - +
180B GLY 4.7 2.9 - - - +
181B GLY* 3.3 9.6 + - - +
183B GLY* 1.3 73.8 - - - +
185B ALA* 1.3 58.0 + - - +
187B ARG* 3.4 17.6 + - - +
188B ARG* 2.8 71.2 + - - +
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Residues in contact with ALA 185 (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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36A VAL* 3.6 8.9 - - + +
171B LEU* 3.4 20.8 - - + +
175B HIS 4.3 2.5 - - - +
176B VAL* 4.2 18.2 - - + -
179B ALA* 3.6 19.4 - - + +
181B GLY 3.0 17.1 + - - +
182B VAL* 3.7 5.8 - - - +
183B GLY 3.3 0.2 - - - -
184B GLU* 1.3 74.8 - - - +
186B VAL* 1.3 65.1 + - + +
189B ALA* 3.1 24.8 + - - +
201B VAL* 5.4 0.4 - - + -
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Residues in contact with VAL 186 (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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171B LEU* 3.8 7.0 - - + -
182B VAL* 2.9 26.8 + - + +
185B ALA* 1.3 75.3 - - - +
187B ARG* 1.3 58.4 + - - +
189B ALA* 3.5 1.3 + - - +
190B LYS* 2.9 36.0 + - + +
199B VAL* 4.6 3.1 - - + -
201B VAL* 3.9 36.8 - - + -
212B ALA* 4.6 0.9 - - - -
215B ALA* 3.5 36.1 - - + +
217B ALA* 3.7 24.2 - - + +
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Residues in contact with ARG 187 (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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183B GLY* 3.0 35.7 + - - +
184B GLU* 3.8 16.3 + - - +
186B VAL* 1.3 74.7 - - - +
188B ARG* 1.3 65.4 + - + +
189B ALA 3.1 1.8 - - - -
190B LYS* 4.0 3.7 - - - +
191B ALA* 3.1 25.6 + - - +
214B GLU* 4.9 7.7 + - - +
215B ALA* 3.9 33.2 - - + +
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Residues in contact with ARG 188 (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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35A LEU 3.9 0.2 - - - +
36A VAL* 3.0 45.0 + - + +
38A PRO* 4.1 17.6 - - - +
178B ALA 4.1 6.1 + - - -
179B ALA* 3.5 31.3 + - - +
184B GLU* 2.8 58.0 + - - +
187B ARG* 1.3 72.7 - - - +
189B ALA* 1.3 61.1 + - - +
191B ALA* 3.6 7.1 + - - +
192B ARG* 3.3 47.5 + - - +
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Residues in contact with ALA 189 (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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35A LEU* 4.2 15.4 - - + +
36A VAL* 3.8 11.1 - - + +
169B ILE* 4.8 2.0 - - + -
171B LEU* 3.9 19.1 - - + -
185B ALA 3.1 19.0 + - - +
186B VAL 3.6 3.8 - - - +
188B ARG* 1.3 74.6 - - - +
190B LYS* 1.3 58.7 + - - +
191B ALA 3.0 5.2 + - - -
192B ARG 3.2 1.9 + - - -
193B ALA* 2.9 34.6 + - - +
199B VAL* 4.0 13.0 - - + -
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Residues in contact with LYS 190 (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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186B VAL* 2.9 25.7 + - + +
187B ARG* 4.4 3.8 - - - +
189B ALA* 1.3 72.2 - - - +
191B ALA* 1.3 60.7 + - - +
192B ARG 3.4 0.4 + - - -
193B ALA* 4.3 5.8 + - - +
199B VAL* 3.7 24.7 - - + -
215B ALA 4.2 9.0 - - - +
216B GLY* 2.9 37.3 + - - +
218B ASP* 3.4 22.5 + - - -
198C LYS* 6.1 1.7 - - - +
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Residues in contact with ALA 191 (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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187B ARG 3.1 19.1 + - - +
188B ARG* 3.6 9.9 - - - +
189B ALA 3.0 0.4 - - - -
190B LYS* 1.3 79.9 - - - +
192B ARG* 1.3 62.0 + - + +
134C GLN* 5.5 0.3 + - - -
159C ARG* 3.0 21.8 + - - -
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Residues in contact with ARG 192 (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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34A LEU 5.0 6.0 + - - -
35A LEU* 2.7 53.3 + - + +
36A VAL* 4.4 3.6 + - - +
38A PRO* 6.4 0.4 - - - +
188B ARG* 3.3 38.3 + - - +
189B ALA 3.2 0.6 + - - -
191B ALA* 1.3 81.1 - - + +
193B ALA* 1.3 64.9 + - - +
194B PRO* 3.9 1.6 - - - +
159C ARG* 3.6 25.9 + - - +
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Residues in contact with ALA 193 (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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35A LEU* 3.8 5.4 - - + -
169B ILE* 3.3 27.1 - - + -
189B ALA 2.9 21.1 + - - +
190B LYS* 4.3 6.0 + - - +
191B ALA 3.9 0.6 - - - -
192B ARG* 1.3 79.5 - - - +
194B PRO* 1.3 74.3 - - - +
195B HIS* 3.2 3.8 + - - -
197B LEU 5.4 0.7 - - - +
199B VAL* 4.1 9.6 - - + -
159C ARG* 4.6 7.0 + - - +
264C TYR* 4.8 4.5 + - - -
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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