Contacts of the helix formed by residues 185 - 197 (chain B) in PDB entry 1D02
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 SER 185 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19B LYS* 4.4 29.9 + - - -
25B GLN* 3.7 9.9 - - - -
180B TRP* 3.0 15.9 + - - -
183B ASN 3.6 3.3 + - - -
184B GLU* 1.3 90.1 + - - +
186B GLY* 1.3 64.6 + - - +
187B GLU* 3.4 19.8 + - - +
188B LYS* 3.5 8.7 + - - +
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Residues in contact with GLY 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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15B LEU* 4.1 6.7 - - - -
25B GLN* 2.7 23.6 + - - +
30B VAL* 3.8 16.6 - - - -
180B TRP* 3.8 15.7 - - - -
185B SER* 1.3 71.3 - - - +
187B GLU* 1.3 65.0 + - - +
189B LEU* 3.0 5.5 + - - +
190B VAL* 3.0 24.4 + - - +
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Residues in contact with GLU 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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12B TRP* 4.1 15.4 - - + -
15B LEU* 3.8 19.6 - - + +
19B LYS* 5.2 8.6 + - + +
185B SER* 3.2 13.6 + - - +
186B GLY* 1.3 76.8 - - - +
188B LYS* 1.3 57.8 + - - +
190B VAL* 3.3 2.6 + - - +
191B GLN* 2.8 59.3 + - + +
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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
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61A ASP* 5.6 6.3 + - - -
65A GLU* 5.1 10.9 - - - +
178B PHE* 3.5 29.0 - - + -
179B MET 5.3 1.8 + - - -
181B ARG* 4.9 16.0 - - - +
184B GLU* 3.6 47.6 + - + +
185B SER* 3.5 2.6 + - - +
186B GLY 3.3 0.6 - - - -
187B GLU* 1.3 78.4 - - - +
189B LEU* 1.3 61.2 - - - +
191B GLN* 3.4 16.8 + - - +
192B HIS* 3.2 17.0 + - - +
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Residues in contact with LEU 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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27B LEU* 4.0 14.8 - - + -
30B VAL* 4.2 8.1 - - + -
31B PHE* 3.7 24.7 - - + -
149B TRP* 3.7 23.2 - - + -
151B VAL* 4.1 17.9 - - + -
178B PHE* 3.6 35.3 - - + -
180B TRP* 3.8 40.4 - - + -
185B SER 4.0 1.2 + - - -
186B GLY 3.0 9.2 + - - +
188B LYS* 1.3 78.3 - - - +
190B VAL* 1.3 62.4 + - - +
192B HIS* 3.2 13.5 + - - +
193B PHE 3.4 8.3 + - - -
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Residues in contact with VAL 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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10B LEU* 3.6 22.7 - - + -
12B TRP* 3.5 25.1 - - + -
15B LEU* 3.9 7.4 - - + -
30B VAL* 3.4 31.2 - - + -
31B PHE* 4.0 18.4 - - + -
34B VAL* 3.8 24.5 - - + -
186B GLY 3.0 11.1 + - - +
187B GLU 3.9 3.1 - - - +
189B LEU* 1.3 73.9 - - - +
191B GLN* 1.3 56.3 + - - +
193B PHE* 3.1 2.8 + - - +
194B ASN* 2.7 32.6 + - - +
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Residues in contact with GLN 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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12B TRP* 3.8 19.8 - - + -
187B GLU* 2.8 48.7 + - + +
188B LYS* 3.7 25.6 + - + +
189B LEU 3.3 0.2 - - - -
190B VAL* 1.3 72.3 - - - +
192B HIS* 1.3 63.7 + - - +
194B ASN* 4.1 3.1 - - - -
195B GLU* 2.9 50.4 + - - +
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Residues in contact with HIS 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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149B TRP* 3.6 26.0 + - + -
174B GLN 4.6 0.8 + - - -
175B ASP* 2.8 36.2 + - + -
177B TYR 3.4 12.6 + - - -
178B PHE* 3.5 35.4 - + + -
188B LYS 3.2 8.6 + - - +
189B LEU 3.5 9.9 - - - +
190B VAL 3.2 0.6 - - - -
191B GLN* 1.3 77.4 - - - +
193B PHE* 1.3 62.0 + - - +
195B GLU* 5.1 1.1 - - - -
196B LYS* 2.9 68.2 + - + +
197B LEU* 3.9 6.2 + - + +
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Residues in contact with PHE 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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10B LEU* 4.2 9.0 - - + -
31B PHE* 4.0 19.7 - + + -
35B PHE* 4.0 17.9 - + - -
40B TYR* 4.5 4.0 - + - -
86B ILE* 3.7 40.4 - - + -
95B LEU* 4.1 12.1 - - + -
149B TRP* 3.9 17.2 - + + -
189B LEU 3.4 2.0 + - - -
190B VAL 3.1 6.4 + - - +
192B HIS* 1.3 79.2 + - - +
194B ASN* 1.3 65.6 + - - +
197B LEU* 2.9 25.2 + - + -
198B LYS* 2.8 69.4 + - + -
201B LEU* 4.1 13.0 - - + -
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Residues in contact with ASN 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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10B LEU* 3.5 20.7 - - + +
12B TRP* 3.7 23.5 + - + +
190B VAL 2.7 20.4 + - - +
191B GLN* 3.7 4.9 - - - +
193B PHE* 1.3 81.1 - - - +
195B GLU* 1.3 66.4 + - + +
198B LYS* 2.8 49.1 + - - +
199B LYS* 5.0 1.9 + - - +
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Residues in contact with GLU 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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191B GLN* 2.9 45.6 + - - +
192B HIS* 5.4 0.5 - - - -
194B ASN* 1.3 81.4 - - - +
196B LYS* 1.3 75.7 + - + +
199B LYS* 4.9 12.9 + - - +
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Residues in contact with LYS 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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145B ILE* 4.5 2.8 - - - +
175B ASP* 3.3 44.3 + - + +
192B HIS* 2.9 44.2 + - + +
195B GLU* 1.3 94.4 - - + +
197B LEU* 1.3 66.8 + - + +
199B LYS* 4.2 8.7 - - - +
200B TYR* 3.6 20.7 - - - -
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Residues in contact with LEU 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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95B LEU* 3.9 22.7 - - + +
145B ILE* 3.9 24.2 - - + -
149B TRP* 3.5 48.7 - - + +
175B ASP 3.6 17.7 - - - +
176B ASN* 4.3 7.4 - - - +
192B HIS* 4.0 7.4 - - + +
193B PHE* 2.9 19.0 + - + +
196B LYS* 1.3 89.8 - - + +
198B LYS* 1.3 67.9 + - - +
199B LYS 3.2 2.9 - - - -
200B TYR* 2.9 26.1 + - + +
201B LEU* 4.0 5.4 + - - +
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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