Contacts of the helix formed by residues 192 - 204 (chain B) in PDB entry 1PN9
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 192 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17B MET* 3.6 8.9 - - - +
20B ALA* 3.8 17.5 - - - +
190B ALA 3.3 0.8 + - - -
191B PRO* 1.3 71.8 - - - +
193B TYR* 1.3 65.2 + - - +
194B ALA* 3.1 4.7 - - - -
195B LEU* 2.9 32.5 + - - +
196B ASN 3.5 2.6 + - - -
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Residues in contact with TYR 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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17B MET* 4.1 11.7 - - - -
160B ALA* 4.5 11.2 - - + -
164B ALA* 3.8 4.9 - - + +
167B GLU* 5.0 0.7 + - - -
183B PHE* 3.2 30.6 - + - -
186B CYS 3.6 15.5 - - - +
187B LYS* 3.5 50.0 - - + +
190B ALA* 3.1 18.9 + - + +
191B PRO 3.2 0.6 - - - -
192B GLY* 1.3 76.8 - - - +
194B ALA* 1.3 51.1 + - - +
196B ASN* 2.7 54.3 + - - +
197B GLN* 2.8 43.5 + - + -
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Residues in contact with ALA 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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192B GLY* 3.1 2.4 + - - -
193B TYR* 1.3 78.8 - - - +
195B LEU* 1.3 60.2 + - + +
197B GLN* 3.8 8.1 - - - +
198B ALA* 3.0 29.6 + - - +
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Residues in contact with LEU 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B PRO* 5.4 1.0 - - - +
13B ARG* 4.0 6.5 - - - +
16B GLN* 4.3 49.3 + - + +
20B ALA* 5.4 3.1 - - + -
28B LEU* 6.0 4.3 - - + -
192B GLY* 2.9 22.6 + - - +
194B ALA* 1.3 78.7 - - + +
196B ASN* 1.3 59.4 + - - +
198B ALA* 4.0 5.1 - - + +
199B GLY* 3.0 24.4 + - - -
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Residues in contact with ASN 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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13B ARG* 2.8 45.0 + - + +
17B MET* 3.6 32.1 - - + +
160B ALA 3.2 19.0 + - - -
161B ALA* 3.4 3.8 - - - -
164B ALA* 3.3 9.1 - - - +
192B GLY 3.5 0.6 + - - -
193B TYR* 2.7 38.4 + - + +
195B LEU* 1.3 78.4 - - - +
197B GLN* 1.3 62.5 + - - +
200B ALA* 3.0 25.1 + - - +
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Residues in contact with GLN 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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164B ALA* 5.8 1.6 - - - -
167B GLU* 4.6 13.4 + - - +
168B VAL* 5.0 6.1 - - - +
187B LYS* 4.9 5.9 + - - +
193B TYR* 2.8 42.3 + - + +
194B ALA* 3.8 10.8 - - - +
196B ASN* 1.3 74.2 - - - +
198B ALA* 1.3 57.1 + - - +
200B ALA* 3.3 4.1 + - - +
201B ASP* 2.9 66.2 + - - +
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Residues in contact with ALA 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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7B PRO* 5.2 1.6 - - + -
194B ALA 3.0 18.6 + - - +
195B LEU* 4.0 6.7 - - + +
197B GLN* 1.3 75.3 - - - +
199B GLY* 1.3 60.6 + - - +
201B ASP* 3.2 10.1 + - - +
202B GLU* 2.9 27.2 + - - +
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Residues in contact with GLY 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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7B PRO* 3.0 39.9 - - - +
8B GLY* 3.4 7.8 - - - -
13B ARG* 3.8 2.2 - - - -
195B LEU 3.0 17.5 + - - -
198B ALA* 1.3 76.2 - - - +
200B ALA* 1.3 56.8 + - - +
202B GLU* 3.1 5.2 + - - +
203B PHE 2.8 23.9 + - - -
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Residues in contact with ALA 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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13B ARG* 3.6 20.2 - - - +
164B ALA* 4.0 17.7 - - + +
168B VAL* 3.7 30.2 - - + +
196B ASN 3.0 19.5 + - - +
197B GLN* 3.6 7.2 - - - +
199B GLY* 1.3 71.9 - - - +
201B ASP* 1.3 65.8 + - - +
203B PHE* 3.1 21.0 + - - +
204B LYS 3.5 3.8 + - - -
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Residues in contact with ASP 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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168B VAL* 4.1 10.9 - - - +
197B GLN* 2.9 55.4 + - - +
198B ALA* 3.2 8.5 + - - +
200B ALA* 1.3 76.3 - - - +
202B GLU* 1.3 62.7 + - - +
204B LYS* 3.3 24.3 + - - +
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Residues in contact with GLU 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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7B PRO* 4.3 21.7 - - + +
8B GLY* 4.7 5.2 - - - +
198B ALA 2.9 14.0 + - - +
199B GLY* 3.2 13.7 - - - +
201B ASP* 1.3 74.9 - - - +
203B PHE* 1.3 53.5 - - - +
205B ALA* 2.7 46.2 + - + +
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Residues in contact with PHE 203 (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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8B GLY* 3.3 29.5 - - - +
13B ARG* 4.8 0.9 - - - +
108B PHE* 4.2 8.3 - + - -
113B TYR* 5.2 5.8 - + - -
116B ILE* 3.9 20.2 - - + -
117B PHE* 5.4 2.0 - + - -
165B THR* 3.7 24.5 - - + -
168B VAL* 4.4 3.1 - - + -
199B GLY 2.8 12.6 + - - +
200B ALA* 3.2 15.9 - - - +
202B GLU* 1.3 76.3 - - - +
204B LYS* 1.3 48.5 + - - +
206B LYS* 2.5 56.5 + - + +
207B PHE* 3.1 43.3 + + - -
302B GTX 3.9 27.1 - - + -
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Residues in contact with LYS 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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168B VAL* 3.3 46.0 - - + +
200B ALA 3.5 1.0 + - - +
201B ASP* 3.3 18.9 + - - +
202B GLU 2.9 1.2 + - - -
203B PHE* 1.3 77.4 - - - +
205B ALA* 1.3 51.1 + - - +
206B LYS 2.8 2.2 - - - -
207B PHE* 2.7 31.3 + - + -
208B LEU* 2.7 50.7 + - + +
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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