Contacts of the helix formed by residues 192 - 208 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A MET* 3.6 10.1 - - - +
20A ALA* 3.9 18.3 - - - +
190A ALA 3.4 0.8 + - - -
191A PRO* 1.3 71.1 - - - +
193A TYR* 1.3 64.5 + - - +
194A ALA* 3.0 5.6 - - - -
195A LEU* 3.0 29.8 + - - +
196A ASN 3.7 0.2 + - - -
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Residues in contact with TYR 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A MET* 3.9 20.4 - - - -
160A ALA* 4.3 12.8 - - + -
164A ALA* 3.9 3.8 - - - +
167A GLU* 5.2 0.2 + - - -
183A PHE* 3.0 31.8 - + - -
186A CYS* 3.9 6.5 - - + -
187A LYS* 3.4 55.9 - - + +
190A ALA* 3.2 18.0 + - + +
191A PRO 3.2 3.2 + - - -
192A GLY* 1.3 77.4 - - - +
194A ALA* 1.3 63.6 + - - +
196A ASN* 2.8 35.6 + - - +
197A GLN* 2.8 38.7 + - + -
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Residues in contact with ALA 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A GLY* 4.6 2.7 - - - +
193A TYR* 1.3 79.3 - - - +
195A LEU* 1.3 60.8 + - + +
197A GLN* 3.3 8.2 + - - +
198A ALA* 2.9 30.0 + - - +
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Residues in contact with LEU 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A PRO* 5.4 1.4 - - - +
13A ARG* 3.9 6.5 - - - +
16A GLN* 4.0 54.7 - - + +
17A MET* 5.6 0.2 - - + -
20A ALA* 5.6 2.7 - - + -
28A LEU* 6.2 2.2 - - + -
192A GLY* 3.0 17.7 + - - +
194A ALA* 1.3 79.6 - - + +
196A ASN* 1.3 59.0 + - - +
198A ALA* 3.8 8.0 - - + +
199A GLY* 3.0 24.9 + - - -
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Residues in contact with ASN 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A ARG* 2.9 44.0 + - + +
17A MET* 3.5 28.1 - - + +
160A ALA 3.3 20.8 + - - -
161A ALA* 3.3 8.3 - - - -
164A ALA* 3.4 11.9 - - - +
192A GLY 3.7 0.8 + - - -
193A TYR* 2.8 37.3 + - + +
195A LEU* 1.3 79.3 - - - +
197A GLN* 1.3 63.2 + - - +
199A GLY 3.3 0.7 + - - -
200A ALA* 3.0 22.7 + - - +
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Residues in contact with GLN 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A ALA* 5.8 0.9 - - - -
167A GLU* 4.9 8.0 + - - +
168A VAL* 5.7 2.0 - - - +
187A LYS* 4.5 12.0 + - - +
193A TYR* 2.8 37.7 + - + +
194A ALA* 3.6 10.8 - - - +
196A ASN* 1.3 77.5 - - - +
198A ALA* 1.3 62.5 + - - +
200A ALA* 3.5 5.4 + - - +
201A ASP* 3.0 60.8 + - - +
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Residues in contact with ALA 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A PRO* 5.1 3.1 - - + -
194A ALA 2.9 17.7 + - - +
195A LEU* 3.8 10.8 - - + +
197A GLN* 1.3 78.3 - - - +
199A GLY* 1.3 60.4 + - - +
201A ASP* 3.5 8.6 + - - +
202A GLU* 3.1 24.9 + - - +
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Residues in contact with GLY 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A PRO* 3.0 36.1 - - - +
8A GLY* 3.5 12.1 - - - -
13A ARG* 3.5 8.7 - - - -
195A LEU 3.0 11.8 + - - -
197A GLN 3.3 0.4 - - - -
198A ALA* 1.3 76.3 - - - +
200A ALA* 1.3 63.9 + - - +
202A GLU* 3.3 2.1 + - - +
203A PHE* 3.0 17.7 + - - +
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Residues in contact with ALA 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A ARG* 3.6 11.0 - - - +
164A ALA* 3.8 34.8 - - + +
165A THR* 4.7 1.3 - - - +
168A VAL* 3.7 14.8 - - + +
196A ASN 3.0 16.1 + - - +
197A GLN* 3.9 7.9 - - - +
199A GLY* 1.3 75.9 - - - +
201A ASP* 1.3 58.9 + - - +
203A PHE* 3.0 10.9 + - - +
204A LYS* 2.9 26.7 + - - +
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Residues in contact with ASP 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A VAL* 4.3 9.1 - - - +
197A GLN* 3.0 44.9 + - - +
198A ALA* 3.7 7.7 - - - +
200A ALA* 1.3 76.7 - - - +
202A GLU* 1.3 56.7 + - - +
204A LYS* 3.1 12.2 + - - +
205A ALA* 3.0 30.5 + - - +
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Residues in contact with GLU 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A LEU* 5.6 1.9 - - - +
7A PRO* 3.0 36.7 - - + +
8A GLY* 4.6 5.8 + - - +
198A ALA 3.1 17.0 + - - +
199A GLY* 3.5 6.7 - - - +
200A ALA 3.3 0.2 - - - -
201A ASP* 1.3 76.5 - - - +
203A PHE* 1.3 58.5 + - - +
205A ALA* 4.6 4.0 - - - +
206A LYS* 3.0 72.7 + - + +
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Residues in contact with PHE 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A GLY* 3.5 25.1 - - - +
13A ARG* 5.0 0.7 - - - +
108A PHE* 4.6 4.9 - + - -
113A TYR* 3.8 31.4 - + - -
116A ILE* 4.0 12.6 - - + -
117A PHE* 5.1 3.4 - + - -
165A THR* 4.0 24.2 - - + -
168A VAL* 4.6 2.9 - - + -
199A GLY 3.0 12.9 + - - +
200A ALA* 3.1 14.1 - - - +
202A GLU* 1.3 78.7 - - - +
204A LYS* 1.3 56.3 + - - +
207A PHE* 3.0 51.1 + + + -
208A LEU* 3.5 33.2 + - + -
301A GTX 3.8 23.1 - - + -
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Residues in contact with LYS 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A VAL* 3.1 43.8 + - + +
200A ALA 2.9 6.8 + - - +
201A ASP* 3.4 14.1 - - - +
203A PHE* 1.3 77.3 - - - +
205A ALA* 1.3 53.4 + - - +
208A LEU* 3.0 22.8 + - + +
209A SER* 2.6 39.0 + - - +
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Residues in contact with ALA 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A ASP 3.0 15.5 + - - +
202A GLU* 4.3 4.3 - - - +
204A LYS* 1.3 75.4 - - + +
206A LYS* 1.3 63.3 + - + +
209A SER* 2.6 27.7 + - - +
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Residues in contact with LYS 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A LEU* 6.0 3.6 - - - +
32A ASP* 5.8 1.6 + - - -
202A GLU* 3.0 56.5 + - + +
205A ALA* 1.3 83.1 - - + +
207A PHE* 1.3 89.4 + - + +
208A LEU 3.8 0.2 - - - -
209A SER 5.2 0.9 - - - -
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Residues in contact with PHE 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A LEU* 6.1 1.1 - - + -
8A GLY* 5.6 2.7 - - - -
34A MET* 4.0 30.5 - - + -
116A ILE* 3.3 36.0 - - + +
117A PHE* 4.8 10.5 - + - -
119A LYS* 5.2 4.5 + - - -
203A PHE* 3.0 41.0 + + + +
206A LYS* 1.3 104.4 - - + +
208A LEU* 1.3 64.1 + - - +
209A SER* 5.3 0.7 - - - -
301A GTX 3.6 34.8 - - + -
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Residues in contact with LEU 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A HIS* 5.8 1.3 - - - +
116A ILE* 3.5 34.8 - - + -
168A VAL* 3.2 45.3 - - + +
169A ALA* 3.9 14.4 - - + -
203A PHE* 3.7 20.2 - - + +
204A LYS* 3.0 19.3 + - + +
207A PHE* 1.3 85.1 - - - +
209A SER* 1.3 65.3 - - - +
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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