Contacts of the helix formed by residues 188 - 201 (chain B) in PDB entry 2X1L
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 PRO 188 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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186B ILE 4.1 0.2 - - - +
187B GLY* 1.3 88.0 - - - +
189B ASP* 1.3 68.4 + - - +
190B ALA* 3.2 6.5 - - + +
191B ARG* 2.9 32.2 + - + +
192B ARG 3.4 7.3 + - - -
290B PHE* 3.5 16.1 - - + -
291B ALA 3.5 20.2 - - - +
334B PHE 5.8 0.2 - - - +
335B GLY* 4.3 16.2 - - - +
603B 2HP 3.4 23.6 - - - +
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Residues in contact with ASP 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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188B PRO* 1.3 70.7 - - - +
190B ALA* 1.3 63.6 + - - +
192B ARG* 2.8 47.9 + - - +
193B ASN* 3.1 34.2 + - - +
603B 2HP 2.8 33.2 + - - +
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Residues in contact with ALA 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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188B PRO* 3.1 7.0 + - + +
189B ASP* 1.3 77.9 - - - +
191B ARG* 1.3 82.6 + - - +
193B ASN* 3.7 10.9 + - - +
194B GLU* 3.3 27.5 + - - +
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Residues in contact with ARG 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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186B ILE* 4.1 14.1 - - + -
187B GLY 4.3 1.3 - - - +
188B PRO* 2.9 31.4 + - + +
190B ALA* 1.3 89.5 - - - +
192B ARG* 1.3 65.8 + - - +
194B GLU* 2.9 46.5 + - - +
195B ILE* 3.1 25.5 + - - +
264B LYS* 4.2 34.6 - - - +
267B ILE* 4.2 14.3 - - + +
291B ALA* 4.2 11.9 + - + +
335B GLY 4.1 17.2 + - - -
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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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179B TYR* 4.3 11.8 + - + +
183B PRO* 3.1 53.4 + - - +
186B ILE* 3.5 44.1 + - + +
188B PRO 3.4 2.6 + - - -
189B ASP* 2.8 50.0 + - - +
191B ARG* 1.3 78.8 - - - +
193B ASN* 1.3 68.0 + - - +
195B ILE* 3.1 3.1 + - - +
196B VAL* 2.8 39.9 + - + +
288B ARG* 6.0 0.2 - - - +
603B 2HP 5.0 0.2 + - - -
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Residues in contact with ASN 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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189B ASP* 3.1 27.7 + - - +
190B ALA* 3.9 9.1 - - - +
192B ARG* 1.3 87.8 + - - +
194B GLU* 1.3 57.6 + - + +
196B VAL* 3.8 9.3 - - - +
197B SER* 3.1 28.2 + - - -
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Residues in contact with GLU 194 (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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190B ALA* 3.3 12.0 + - - +
191B ARG* 2.9 52.5 + - - +
192B ARG 3.2 0.4 - - - -
193B ASN* 1.3 76.0 - - + +
195B ILE* 1.3 61.3 + - + +
197B SER* 3.5 6.4 + - - -
198B PHE* 3.0 27.7 + - - +
267B ILE* 5.8 2.9 - - - +
268B ARG* 5.4 2.4 + - - +
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Residues in contact with ILE 195 (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 TYR* 3.6 33.2 - - + +
186B ILE* 3.8 15.3 - - + -
191B ARG 3.1 15.6 + - - +
192B ARG 3.1 7.5 + - - +
194B GLU* 1.3 76.4 - - + +
196B VAL* 1.3 65.2 + - - +
198B PHE* 3.1 4.5 + - + +
199B VAL* 2.9 24.7 + - - +
267B ILE* 3.8 22.9 - - + -
268B ARG* 3.8 28.3 - - + +
271B THR* 3.4 24.0 - - - +
272B VAL* 3.9 9.6 - - + -
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Residues in contact with VAL 196 (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 LEU* 3.8 8.7 - - + +
179B TYR* 3.9 36.8 - - + -
192B ARG* 2.8 32.0 + - + +
193B ASN* 3.8 10.5 - - - +
195B ILE* 1.3 71.1 - - - +
197B SER* 1.3 55.5 + - - +
200B SER* 2.7 45.7 + - - +
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Residues in contact with SER 197 (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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193B ASN 3.1 20.1 + - - -
194B GLU* 3.6 7.9 - - - -
196B VAL* 1.3 77.7 - - - +
198B PHE* 1.3 61.5 + - - +
200B SER* 3.6 6.6 + - - -
201B GLY* 3.6 14.7 + - - -
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Residues in contact with PHE 198 (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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194B GLU 3.0 17.7 + - - +
195B ILE* 3.1 6.9 + - + +
197B SER* 1.3 75.0 - - - +
199B VAL* 1.3 71.5 + - + +
201B GLY* 3.5 11.4 + - - -
202B GLY 4.2 10.2 - - - +
203B LEU* 3.7 27.5 - - + +
268B ARG* 3.6 61.7 - - + +
272B VAL* 4.3 14.4 - - + -
273B TYR* 5.4 10.1 - + - -
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Residues in contact with VAL 199 (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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172B THR* 3.4 37.1 - - + +
175B LEU* 4.3 6.1 - - + -
176B LEU* 3.8 17.0 - - + -
179B TYR* 3.7 23.1 - - + +
195B ILE 2.9 20.3 + - - +
198B PHE* 1.3 76.2 - - + +
200B SER* 1.3 64.4 + - - +
202B GLY* 3.1 13.0 + - - -
203B LEU* 3.9 22.0 - - + -
272B VAL* 3.9 25.6 - - + -
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Residues in contact with SER 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B THR* 5.7 0.5 - - - +
176B LEU* 3.5 23.9 - - - +
196B VAL* 2.7 30.5 + - - +
197B SER* 3.8 8.9 - - - -
198B PHE 3.3 0.4 - - - -
199B VAL* 1.3 77.2 - - - +
201B GLY* 1.3 56.3 + - - +
202B GLY* 3.1 3.5 + - - -
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Residues in contact with GLY 201 (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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197B SER 3.6 6.4 + - - -
198B PHE 3.5 8.7 + - - -
199B VAL 3.2 1.2 - - - -
200B SER* 1.3 77.0 - - - +
202B GLY* 1.3 63.7 + - - +
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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