Contacts of the helix formed by residues 136 - 148 (chain P) in PDB entry 1PP9
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 136 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63P PHE* 4.2 3.1 - - - -
134P PRO* 3.4 2.8 - - - -
135P TRP* 1.3 82.3 - - - +
137P GLN* 1.3 65.3 + - - -
139P SER* 3.1 7.8 + - - -
140P PHE 3.1 15.1 + - - -
255P ASN* 3.2 22.4 - - - -
257P THR 3.1 14.1 - - - -
258P PRO* 4.0 2.5 - - - -
259P ALA* 3.6 7.7 - - - +
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Residues in contact with GLN 137 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136P GLY* 1.3 72.1 - - - -
138P MET* 1.3 66.5 + - + +
140P PHE* 3.4 2.1 + - - +
141P TRP* 3.0 49.9 + - - -
254P ASP* 3.4 13.3 + - + +
255P ASN* 3.4 1.4 + - - -
257P THR* 2.7 27.2 + - + +
258P PRO 3.6 12.8 - - - +
259P ALA* 3.9 1.3 - - - +
260P ASN* 2.9 36.6 + - - +
263P ASN* 2.9 28.4 + - - -
265P PRO* 3.5 26.7 - - + +
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Residues in contact with MET 138 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131P TYR* 3.6 33.6 - - + +
137P GLN* 1.3 73.5 - - - +
139P SER* 1.3 60.6 + - - +
141P TRP* 4.6 0.4 - - - +
142P GLY* 2.8 30.1 + - - -
252P ASP* 3.8 28.3 - - - +
254P ASP* 3.7 24.9 - - + +
255P ASN* 2.8 19.5 + - - +
265P PRO* 3.8 21.5 - - + -
268P ILE* 3.7 37.7 - - + -
269P LYS 4.0 10.1 - - - +
3001P SMA 3.7 8.5 - - - +
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Residues in contact with SER 139 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131P TYR* 2.6 27.4 + - - -
132P VAL* 3.2 32.3 - - - +
134P PRO* 3.5 0.5 - - - +
135P TRP* 3.3 8.7 + - - -
136P GLY 3.1 25.6 + - - -
138P MET* 1.3 75.9 - - - +
140P PHE* 1.3 57.7 + - - +
142P GLY* 3.9 0.2 - - - -
143P ALA* 3.0 29.5 + - - +
255P ASN* 2.9 16.4 + - - -
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Residues in contact with PHE 140 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93E GLY 5.7 2.2 - - - -
135P TRP* 3.7 30.7 - + + -
136P GLY 3.1 4.4 + - - +
137P GLN 3.8 3.6 - - - +
138P MET 3.3 0.2 - - - -
139P SER* 1.3 81.6 - - - +
141P TRP* 1.3 96.5 + + + +
143P ALA* 3.4 5.7 + - - +
144P THR* 3.0 41.8 + - - -
169P SER* 6.0 1.8 - - - -
170P VAL* 3.6 39.4 - - + +
259P ALA* 3.6 28.0 - - + -
260P ASN 4.8 0.7 - - - -
261P PRO* 3.7 28.7 - - + -
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Residues in contact with TRP 141 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95E PRO* 5.9 0.7 - - + -
143E GLY 3.7 21.1 - - - -
144E CYS* 3.8 12.1 - - - -
145E VAL* 3.3 20.6 - - + -
137P GLN* 3.0 48.2 + - - +
138P MET 4.5 0.2 - - - +
140P PHE* 1.3 95.6 - + - +
142P GLY* 1.3 60.5 + - - +
144P THR* 3.6 15.6 - - + -
145P VAL* 3.0 34.1 + - - +
260P ASN 3.3 18.1 + - - -
261P PRO 3.5 14.6 - - - -
263P ASN 3.2 12.8 + - - -
264P THR* 3.3 23.6 - - + -
265P PRO* 3.7 15.7 - - + -
268P ILE* 3.5 22.9 - - + -
3001P SMA 4.5 1.8 - - - -
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Residues in contact with GLY 142 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128P PHE* 3.4 8.8 - - - -
131P TYR* 6.0 2.0 - - - -
132P VAL* 5.5 0.7 - - - -
138P MET 2.8 19.1 + - - -
139P SER 3.9 0.4 - - - -
141P TRP* 1.3 74.6 - - - +
143P ALA* 1.3 64.9 + - - +
145P VAL* 4.9 0.2 - - - -
146P ILE* 3.1 31.8 + - - +
3001P SMA 3.6 26.1 - - - -
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Residues in contact with ALA 143 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128P PHE* 3.8 13.1 - - - -
132P VAL* 3.8 21.1 - - + +
139P SER 3.0 17.9 + - - +
140P PHE* 3.6 5.6 - - - +
141P TRP 3.3 0.2 - - - -
142P GLY* 1.3 77.8 - - - +
144P THR* 1.3 61.6 + - - +
147P THR* 2.9 31.6 + - - +
165P TRP* 4.0 1.3 + - - +
170P VAL* 4.2 20.9 - - + -
174P THR* 5.1 2.2 - - + -
178P PHE* 4.5 8.5 - - + -
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Residues in contact with THR 144 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142E LEU 3.7 9.2 - - - +
143E GLY* 3.6 29.4 - - - +
144E CYS 4.5 0.4 - - - +
140P PHE* 3.0 32.4 + - - -
141P TRP* 3.6 17.9 - - + -
142P GLY 3.2 0.2 - - - -
143P ALA* 1.3 77.9 - - - +
145P VAL* 1.3 64.0 + - + +
148P ASN* 3.2 33.3 + - - +
165P TRP* 3.9 8.9 - - + -
170P VAL* 3.7 15.5 - - - +
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Residues in contact with VAL 145 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142E LEU* 3.4 24.2 - - + +
144E CYS* 3.4 31.6 - - - -
161E HIS* 3.7 18.4 - - + -
141P TRP 3.0 17.9 + - - +
142P GLY 4.3 0.9 - - - +
144P THR* 1.3 74.5 - - - +
146P ILE* 1.3 64.7 + - - +
148P ASN* 3.0 14.6 + - - +
149P LEU* 3.3 10.9 + - + +
3001P SMA 3.5 46.4 - - + +
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Residues in contact with ILE 146 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128P PHE* 3.4 48.5 - - + -
142P GLY* 3.1 14.1 + - - +
145P VAL* 1.3 72.4 - - + +
147P THR* 1.3 68.1 + - - +
149P LEU* 3.1 27.1 + - + +
150P LEU* 4.4 1.6 + - - +
274P PHE* 4.8 1.8 - - + -
3001P SMA 3.6 92.9 - - + +
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Residues in contact with THR 147 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128P PHE* 4.2 1.7 - - - -
143P ALA 2.9 19.3 + - - -
146P ILE* 1.3 78.0 - - - +
148P ASN* 1.3 63.8 + - - +
149P LEU 3.1 1.2 + - - -
150P LEU* 3.1 21.7 + - + +
161P VAL* 3.6 13.9 - - + +
164P ILE* 3.7 25.6 - - + -
165P TRP* 3.3 35.9 + - + +
178P PHE* 3.9 19.9 - - - -
3001P SMA 4.2 15.3 - - + +
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Residues in contact with ASN 148 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141E HIS 5.3 0.2 - - - -
142E LEU* 3.0 44.8 + - + +
143E GLY* 3.7 8.7 - - - +
144P THR* 3.2 18.9 + - - +
145P VAL 3.0 7.4 + - - +
147P THR* 1.3 74.1 - - - +
149P LEU* 1.3 63.4 + - - +
150P LEU 2.9 2.2 - - - -
151P SER* 2.6 35.5 + - - +
152P ALA 4.1 0.2 + - - -
161P VAL* 3.7 20.8 - - - +
165P TRP* 3.7 19.7 - - - -
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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