Contacts of the helix formed by residues 195 - 208 (chain A) in PDB entry 4PJW
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 TYR 195 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106A TYR* 3.8 14.1 - - - +
110A ARG* 3.9 41.7 - - + +
111A ASP* 2.4 31.9 + - - -
114A LEU* 3.3 32.1 - - + -
136A PHE* 4.1 12.6 - + - -
193A ASP* 2.8 9.4 + - - +
194A GLU* 1.3 81.6 - - - +
196A MSE 1.3 65.0 + - - +
197A MSE 3.5 2.1 - - - +
198A ASP* 3.7 2.1 + - - +
199A THR* 3.0 33.1 + - - -
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Residues in contact with MSE 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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102A TRP* 3.9 23.3 - - + -
106A TYR* 3.5 18.4 - - + +
114A LEU* 3.9 24.5 - - + +
117A LEU* 4.9 2.9 - - - -
182A LEU* 4.3 12.8 - - + +
183A VAL* 5.7 1.3 - - + -
186A CYS* 3.2 39.0 - - + -
190A ILE* 3.7 20.4 - - + +
191A ILE* 5.3 0.9 - - + -
193A ASP* 3.0 8.2 + - - +
195A TYR* 1.3 81.1 - - - +
197A MSE 1.3 85.8 + - + +
199A THR* 3.6 2.8 - - - -
200A VAL* 3.3 36.5 + - - +
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Residues in contact with MSE 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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183A VAL* 4.6 8.1 - - - -
191A ILE* 3.7 37.9 - - + +
193A ASP* 4.8 1.2 + - - -
195A TYR 3.5 1.0 - - - +
196A MSE 1.3 97.4 - - - +
198A ASP* 1.3 63.7 + - - +
200A VAL* 3.4 5.2 + - + +
201A ILE* 2.8 51.2 + - + +
226A LEU* 3.8 33.0 - - + -
230A LEU* 4.0 12.6 - - + -
284A MSE 3.6 35.7 - - + -
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Residues in contact with ASP 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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194A GLU* 3.7 30.4 - - - +
195A TYR 3.7 4.9 + - - +
196A MSE 3.5 0.4 - - - -
197A MSE 1.3 79.5 + - - +
199A THR* 1.3 59.6 + - - +
201A ILE* 4.1 4.8 - - - +
202A SER* 2.5 40.5 + - - +
280A GLU* 5.6 1.6 - - - +
284A MSE 4.9 9.4 - - - +
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Residues in contact with THR 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A LEU* 3.6 26.1 - - + +
118A ILE* 3.6 28.0 - - + -
136A PHE* 5.0 8.2 - - + -
141A ASN* 4.8 0.9 + - - -
195A TYR* 3.0 24.0 + - - -
196A MSE 3.6 4.9 - - - +
198A ASP* 1.3 80.1 - - - +
200A VAL* 1.3 65.4 + - + +
202A SER* 3.6 4.1 - - - -
203A LEU* 3.1 22.5 + - - +
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Residues in contact with VAL 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A LEU* 4.7 3.1 - - + -
117A LEU* 3.4 35.0 - - + -
118A ILE* 5.5 3.4 - - + -
121A PHE* 3.7 26.5 - - + -
196A MSE 3.3 23.8 + - - +
197A MSE 3.9 8.5 - - - +
199A THR* 1.3 81.2 - - + +
201A ILE* 1.3 59.9 + - - +
203A LEU* 3.4 5.7 + - - +
204A LEU* 3.0 31.9 + - + +
226A LEU* 4.0 25.4 - - + -
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Residues in contact with ILE 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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197A MSE 2.8 36.2 + - + +
198A ASP* 4.1 4.7 - - - +
200A VAL* 1.3 69.9 - - - +
202A SER* 1.3 58.4 + - - +
204A LEU* 3.8 5.2 - - - +
205A THR* 2.5 48.5 + - - +
226A LEU* 4.0 10.5 - - + -
284A MSE 3.9 35.0 - - + +
287A ALA* 4.3 16.2 - - + -
288A ILE* 3.7 39.3 - - + -
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Residues in contact with SER 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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141A ASN* 3.5 21.0 + - - -
198A ASP* 2.5 28.9 + - - +
199A THR* 3.6 5.1 - - - -
201A ILE* 1.3 79.0 - - - +
203A LEU* 1.3 62.1 + - - +
205A THR* 3.4 6.7 + - - -
206A GLY* 3.0 18.9 + - - -
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Residues in contact with LEU 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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118A ILE* 3.7 55.0 - - + +
121A PHE* 4.5 13.5 - - + -
122A ILE* 5.0 6.5 - - + -
141A ASN* 3.5 30.2 - - + +
144A ILE* 5.4 7.2 - - + -
145A ILE* 4.6 9.3 - - + +
199A THR 3.1 16.4 + - - +
200A VAL* 3.8 4.7 - - - +
202A SER* 1.3 78.4 - - - +
204A LEU* 1.3 58.2 + - + +
206A GLY* 3.1 2.4 + - - -
207A LEU* 2.8 57.0 + - + +
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Residues in contact with LEU 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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121A PHE* 3.9 35.7 - - + -
200A VAL* 3.0 25.3 + - + +
201A ILE* 4.0 4.7 - - - +
203A LEU* 1.3 79.8 - - + +
205A THR* 1.3 56.6 + - - +
207A LEU* 4.6 3.6 - - + -
208A SER* 2.9 31.7 + - - -
219A SER* 3.7 18.9 + - - +
222A ALA* 3.7 17.7 - - + -
223A ALA* 3.6 42.2 - - + +
226A LEU* 4.0 19.3 - - + -
292A VAL* 4.4 2.8 - - + +
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Residues in contact with THR 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 ILE* 2.5 34.7 + - - +
202A SER* 3.6 6.7 - - - -
203A LEU 3.2 0.2 - - - -
204A LEU* 1.3 78.5 - - - +
206A GLY* 1.3 59.3 + - - +
208A SER* 2.9 18.6 + - - -
209A ASP* 3.5 10.9 + - - +
287A ALA 5.2 3.3 + - - -
288A ILE* 5.5 1.0 - - - +
291A GLY* 4.0 29.0 - - - +
292A VAL* 4.1 10.0 - - - +
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Residues in contact with GLY 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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141A ASN* 5.7 2.9 - - - -
145A ILE* 3.5 19.2 - - - +
202A SER 3.0 13.7 + - - -
203A LEU* 3.1 3.1 + - - -
205A THR* 1.3 74.8 - - - +
207A LEU* 1.3 59.5 + - - +
208A SER 3.2 0.2 - - - -
209A ASP* 3.0 22.6 + - - +
210A SER* 3.3 8.8 + - - -
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Residues in contact with LEU 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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121A PHE* 4.9 10.1 - - + +
122A ILE* 4.1 18.6 - - + -
125A SER* 5.6 1.1 - - - +
145A ILE* 3.6 23.1 - - + +
203A LEU* 2.8 42.4 + - + +
204A LEU* 4.6 5.8 - - + -
206A GLY* 1.3 71.1 - - - +
208A SER* 1.3 61.6 + - - +
209A ASP 3.0 4.7 - - - -
210A SER* 3.1 20.0 + - - +
215A PHE* 3.6 39.7 - - + +
216A ARG* 3.4 13.2 + - - -
219A SER* 3.2 24.9 - - - -
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Residues in contact with SER 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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204A LEU 2.9 15.3 + - - -
205A THR 2.9 17.8 + - - -
207A LEU* 1.3 75.2 - - - +
209A ASP* 1.3 56.8 + - - +
210A SER 3.5 0.2 - - - -
216A ARG* 3.3 17.7 - - - +
219A SER* 2.9 15.5 + - - -
220A THR* 4.0 14.1 - - - -
291A GLY 4.2 5.4 + - - -
292A VAL* 3.6 26.6 - - - +
296A ARG* 3.3 26.2 + - - -
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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