Contacts of the helix formed by residues 187 - 204 (chain B) in PDB entry 1XVI
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 187 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72B ASN 3.2 14.4 + - - -
73B GLY* 3.7 3.4 + - - +
171B GLN* 4.9 1.3 - - - -
173B MET* 6.4 1.6 - - - -
186B ALA* 1.3 79.2 - - - +
188B LYS* 1.3 60.4 + - - -
189B ASP* 3.2 14.1 - - - -
190B GLN* 3.1 5.8 + - - +
191B ALA* 2.9 30.3 + - - +
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Residues in contact with LYS 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B ASP* 2.7 37.0 + - - +
46B CYS* 3.3 20.6 - - - -
47B SER 3.7 20.2 - - - -
48B SER* 4.2 7.9 - - - +
69B ILE* 4.0 10.6 - - + +
72B ASN* 3.3 40.9 + - - +
187B GLY* 1.3 71.1 - - - +
189B ASP* 1.3 57.7 + - - +
191B ALA* 3.5 1.7 + - - +
192B ALA* 2.9 29.8 + - - +
218B ASP* 4.5 3.4 + - - -
220B PRO* 5.7 3.1 - - + +
221B LEU* 3.8 18.7 - - + +
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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
----------------------------------------------------------
187B GLY* 3.5 12.6 - - - -
188B LYS* 1.3 72.9 + - - +
190B GLN* 1.3 80.7 + - - +
192B ALA* 3.6 5.9 - - - +
193B ASN* 2.8 37.2 + - - +
220B PRO* 3.6 37.0 - - - +
221B LEU* 4.3 6.9 - - - +
224B VAL* 3.9 16.0 - - + +
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Residues in contact with GLN 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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185B SER 4.0 19.3 + - - +
186B ALA* 4.2 2.5 - - - +
187B GLY* 3.1 20.1 + - - +
189B ASP* 1.3 99.2 + - - +
191B ALA* 1.3 64.3 + - - +
193B ASN* 3.2 17.1 + - - +
194B TRP* 3.1 21.7 + - - +
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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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69B ILE* 3.6 32.8 - - + -
73B GLY* 3.9 7.2 + - - +
76B ILE* 3.8 30.5 - - + +
187B GLY 2.9 15.9 + - - +
188B LYS 3.8 0.7 - - - +
190B GLN* 1.3 76.2 - - - +
192B ALA* 1.3 61.6 + - - +
194B TRP* 3.1 4.9 + - - +
195B ILE* 3.0 26.0 + - - +
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Residues in contact with ALA 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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11B PHE* 3.9 11.2 - - + -
69B ILE* 3.7 8.9 - - + +
188B LYS 2.9 19.3 + - - +
189B ASP 3.6 4.9 - - - +
191B ALA* 1.3 75.1 - - - +
193B ASN* 1.3 57.0 + - - +
194B TRP 3.2 0.2 + - - -
195B ILE* 3.3 2.1 + - - +
196B ILE* 2.8 36.5 + - - +
221B LEU* 3.7 21.3 - - + -
224B VAL* 4.2 3.6 - - + -
225B MET* 3.8 17.3 - - + -
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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* 2.8 20.7 + - - +
190B GLN* 3.2 19.5 + - - +
192B ALA* 1.3 76.7 - - - +
194B TRP* 1.3 56.6 + - - +
196B ILE* 3.5 9.4 + - - +
197B ALA* 3.0 28.8 + - - +
224B VAL* 3.7 28.6 - - - +
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Residues in contact with TRP 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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76B ILE* 4.1 29.6 - - + -
78B LEU* 3.9 11.7 - - + -
82B TRP* 3.9 18.2 - + - -
85B ILE* 3.8 28.0 - - + -
86B ASP 4.3 2.7 - - - -
91B ILE* 3.5 29.2 - - + +
190B GLN 3.1 12.5 + - - +
191B ALA* 3.1 10.0 + - - +
193B ASN* 1.3 72.3 - - - +
195B ILE* 1.3 72.2 + - + +
197B ALA* 3.3 9.0 + - + +
198B THR* 2.9 50.5 + - - -
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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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11B PHE* 3.8 19.5 - - + -
44B ILE* 4.1 10.3 - - + -
67B PRO* 4.1 20.2 - - + -
68B LEU 4.5 1.3 - - - +
69B ILE* 3.5 36.1 - - + -
76B ILE* 4.0 15.9 - - + -
82B TRP* 4.1 5.1 - - + -
191B ALA 3.0 11.9 + - - +
192B ALA 3.6 6.5 - - - +
194B TRP* 1.3 89.6 - - + +
196B ILE* 1.3 65.2 + - - +
198B THR* 3.2 5.2 + - - -
199B TYR* 3.1 45.1 + - + -
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Residues in contact with ILE 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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9B LEU* 4.5 8.1 - - + -
11B PHE* 3.7 20.4 - - + -
192B ALA* 2.8 30.2 + - + +
193B ASN* 3.7 13.2 - - - +
195B ILE* 1.3 71.8 - - - +
197B ALA* 1.3 62.5 + - - +
198B THR 3.3 0.3 + - - -
199B TYR 3.3 1.4 + - - -
200B GLN* 3.0 22.3 + - + +
207B PRO* 3.5 30.7 - - + +
209B THR* 3.8 25.1 - - + +
224B VAL* 4.7 7.6 - - + +
225B MET* 4.2 13.0 - - + -
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Residues in contact with ALA 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 3.0 18.1 + - - +
194B TRP* 3.6 9.4 - - + +
195B ILE 3.3 0.2 - - - -
196B ILE* 1.3 76.3 - - - +
198B THR* 1.3 58.3 + - - +
200B GLN* 3.3 11.8 + - - +
201B GLN* 3.0 29.3 + - - +
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Residues in contact with THR 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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82B TRP* 3.7 36.8 - - + -
85B ILE* 3.8 28.9 - - + +
194B TRP* 2.9 38.2 + - - -
195B ILE 3.6 5.4 - - - -
196B ILE 3.2 0.2 - - - -
197B ALA* 1.3 74.4 - - - +
199B TYR* 1.3 65.5 + - - +
200B GLN 3.2 0.2 + - - -
201B GLN* 3.3 4.8 + - - +
202B LEU* 3.0 26.8 + - + +
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Residues in contact with TYR 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B PRO* 3.9 13.2 - - + +
9B LEU* 3.5 36.6 - - + -
40B ASN* 6.1 1.1 - - - -
42B PRO* 3.9 20.2 - - + +
44B ILE* 4.2 3.5 - - + +
66B LEU* 4.6 3.1 - - - +
67B PRO* 3.3 25.5 - - + +
79B ALA* 4.9 1.9 - - - +
82B TRP* 3.6 32.5 - + - -
195B ILE* 3.1 36.5 + - + -
196B ILE 3.8 6.5 - - - +
198B THR* 1.3 75.6 - - - +
200B GLN* 1.3 51.0 + - - +
202B LEU* 4.1 5.4 - - + +
203B SER* 2.7 39.7 + - - -
207B PRO* 4.0 12.8 - - + -
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Residues in contact with GLN 200 (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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196B ILE* 3.0 16.9 + - - +
197B ALA* 3.5 14.1 - - - +
198B THR 3.1 0.2 - - - -
199B TYR* 1.3 75.6 - - - +
201B GLN* 1.3 61.2 + - - +
204B GLY* 2.9 29.1 + - - -
205B LYS 3.6 19.0 + - - +
206B ARG* 3.7 29.3 - - - +
207B PRO* 3.5 10.1 - - + +
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Residues in contact with GLN 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 ALA 3.0 16.3 + - - +
198B THR* 4.1 4.3 - - - +
200B GLN* 1.3 74.8 - - - +
202B LEU* 1.3 70.3 + - + +
204B GLY* 3.8 5.2 + - - -
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Residues in contact with LEU 202 (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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4B ILE* 3.6 18.6 - - + +
82B TRP* 3.2 45.1 - - + +
84B GLU* 3.3 30.1 - - - +
85B ILE* 4.1 13.7 - - + -
198B THR* 3.0 25.4 + - + +
199B TYR* 4.1 5.8 - - + +
201B GLN* 1.3 82.8 - - + +
203B SER* 1.3 60.2 + - - +
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Residues in contact with SER 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B ILE* 3.9 35.6 - - - +
5B GLN 4.1 3.4 - - - -
7B PRO* 3.4 20.5 - - - +
199B TYR 2.7 23.0 + - - -
202B LEU* 1.3 77.8 - - - +
204B GLY* 1.3 57.8 + - - +
205B LYS* 3.1 37.5 + - - +
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Residues in contact with GLY 204 (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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200B GLN* 2.9 15.9 + - - -
201B GLN 3.8 3.9 + - - -
202B LEU 3.5 2.0 - - - -
203B SER* 1.3 76.3 - - - +
205B LYS* 1.3 62.8 + - - +
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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