Contacts of the helix formed by residues 141 - 153 (chain D) in PDB entry 1P4A
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 141 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109D LEU* 5.1 0.2 - - - -
136D THR* 4.0 14.1 + - - -
137D VAL 4.7 3.7 + - - -
139D THR 3.3 1.0 - - - -
140D LYS* 1.3 78.4 - - - +
142D ILE* 1.3 64.2 + - - +
143D PRO* 3.5 1.1 - - - -
144D LEU* 3.3 12.0 + - - +
145D ALA* 3.0 22.2 + - - +
202D ILE* 5.1 1.2 - - - +
203D ASP* 5.2 1.1 - - - -
204D ASP* 4.0 24.7 + - - -
607D PCP 4.0 5.9 + - - -
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Residues in contact with ILE 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139C THR* 3.8 22.2 - - + +
142C ILE* 3.7 36.3 - - + -
143C PRO* 4.0 4.0 - - + -
136D THR* 4.0 20.0 - - + -
138D ALA* 3.9 19.3 - - + -
139D THR* 3.5 15.0 - - - +
140D LYS 3.2 0.4 - - - -
141D GLY* 1.3 76.7 - - - +
143D PRO* 1.3 73.1 - - + +
145D ALA* 2.9 13.3 + - - +
146D TYR* 2.9 30.0 + - + -
158D ILE* 3.9 22.9 - - + -
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Residues in contact with PRO 143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142C ILE* 3.8 19.5 - - + -
143C PRO* 6.3 0.2 - - + -
146C TYR* 4.1 24.3 - - + -
156C VAL* 5.6 5.2 - - + -
158C ILE* 4.2 11.2 - - + -
109D LEU 3.8 20.2 - - - +
110D GLY* 5.5 1.6 - - - -
115D LEU* 3.8 16.4 - - + -
139D THR 4.2 1.8 - - - +
140D LYS 3.4 15.3 - - - +
142D ILE* 1.3 96.0 - - + +
144D LEU* 1.3 56.4 + - - +
146D TYR* 3.2 5.2 + - + +
147D ALA* 2.9 30.3 + - - +
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Residues in contact with LEU 144 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109D LEU* 4.2 13.2 + - + -
115D LEU* 3.9 22.1 - - + +
118D VAL* 3.6 29.4 - - + -
119D GLY 4.6 4.3 - - - +
122D PHE* 3.6 19.3 - - + -
141D GLY* 3.3 13.9 + - - +
143D PRO* 1.3 79.7 - - - +
145D ALA* 1.3 62.0 + - - +
147D ALA* 3.5 1.8 + - - +
148D ALA* 3.3 19.1 + - - +
202D ILE* 4.3 4.9 - - + +
203D ASP 3.9 23.1 - - - +
204D ASP* 4.0 14.6 - - + -
232D LEU* 4.1 17.3 - - + -
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Residues in contact with ALA 145 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134D VAL* 3.7 19.4 - - + +
136D THR* 3.6 33.9 - - + -
141D GLY 3.0 6.6 + - - +
142D ILE* 2.9 9.2 + - - +
144D LEU* 1.3 77.6 - - - +
146D TYR* 1.3 56.6 + - - +
148D ALA* 3.5 0.7 + - - +
149D ALA* 3.0 28.9 + - - +
156D VAL* 3.5 11.2 - - + +
202D ILE* 4.1 12.5 - - + +
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Residues in contact with TYR 146 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109C LEU 2.4 22.1 + - - -
110C GLY* 2.8 20.4 - - - -
111C LYS 5.3 0.2 - - - -
112C PRO* 5.7 3.4 - - + -
115C LEU* 2.9 32.3 - - + -
143C PRO* 2.8 36.3 - - + +
146C TYR* 4.2 17.7 - - + -
142D ILE* 2.9 24.1 + - + +
143D PRO* 3.2 6.5 + - + +
145D ALA* 1.3 75.3 - - - +
147D ALA* 1.3 58.7 + - - +
149D ALA* 3.7 2.2 - - + +
150D SER* 2.8 31.4 + - - -
156D VAL* 3.3 40.2 + - + +
158D ILE* 4.2 6.3 - - + +
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Residues in contact with ALA 147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146C TYR* 3.5 23.9 - - + +
115D LEU* 3.4 29.2 - - + +
116D SER* 4.6 2.7 - - - +
119D GLY* 4.1 6.1 - - - -
143D PRO 2.9 15.1 + - - +
144D LEU* 3.8 5.4 - - - +
145D ALA 3.3 0.4 - - - -
146D TYR* 1.3 75.5 - - - +
148D ALA* 1.3 59.4 - - - +
150D SER* 2.5 24.4 + - - -
151D TYR* 3.3 13.9 - - + -
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Residues in contact with ALA 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119D GLY* 3.6 23.8 - - - +
122D PHE* 4.1 22.0 - - + -
134D VAL* 4.9 2.0 - - + -
144D LEU 3.3 13.9 + - - +
145D ALA 3.8 3.4 - - - +
147D ALA* 1.3 77.3 - - - +
149D ALA* 1.3 63.6 + - - +
151D TYR* 3.3 5.1 + - - +
152D LEU* 3.2 34.0 + - + +
200D LEU* 5.1 0.2 - - + -
202D ILE* 4.4 13.2 - - + -
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Residues in contact with ALA 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112C PRO* 4.6 1.7 - - + +
134D VAL* 3.8 19.0 - - + +
145D ALA 3.0 8.2 + - - +
146D TYR* 3.8 4.5 - - + +
147D ALA 3.3 0.2 - - - -
148D ALA* 1.3 75.6 - - - +
150D SER* 1.3 58.4 + - - +
152D LEU* 3.2 1.0 + - - -
153D ASN* 2.8 25.6 + - - -
154D VAL* 3.2 27.9 + - - +
156D VAL* 3.2 34.8 - - + -
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Residues in contact with SER 150 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112C PRO* 4.4 18.1 - - - +
146C TYR* 5.5 2.3 - - - -
20D PRO* 3.6 13.3 - - - +
146D TYR 2.8 15.4 + - - -
147D ALA* 2.5 26.3 + - - -
149D ALA* 1.3 78.0 - - - +
151D TYR* 1.3 65.4 + - - +
152D LEU 3.5 0.2 + - - -
153D ASN* 3.5 7.6 + - - -
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Residues in contact with TYR 151 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C THR* 5.8 4.2 - - - +
20D PRO* 3.4 16.6 - - + +
21D HIS* 3.2 19.5 - - - -
71D TYR* 5.6 2.5 - + - -
73D PRO* 3.6 25.6 - - + +
116D SER* 3.1 49.3 + - - -
119D GLY* 3.8 1.1 - - - -
120D LYS* 3.5 36.4 - - + +
123D ALA* 3.4 21.1 - - + -
147D ALA* 3.3 23.3 + - + -
148D ALA 3.3 2.2 + - - +
150D SER* 1.3 82.4 + - - +
152D LEU* 1.3 59.4 + - - +
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Residues in contact with LEU 152 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D HIS* 3.6 39.4 - - + +
122D PHE 5.0 0.4 - - - +
123D ALA* 3.7 35.2 - - + +
126D PHE* 4.5 6.1 - - + +
127D ALA* 4.4 7.0 - - - +
131D ILE* 4.4 16.4 - - + -
134D VAL* 4.7 3.6 - - + -
148D ALA* 3.2 26.1 + - + +
149D ALA 3.2 4.0 + - - +
151D TYR* 1.3 76.2 - - - +
153D ASN* 1.3 70.8 + - - +
154D VAL* 3.8 18.5 - - + +
200D LEU* 4.0 26.7 - - + -
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Residues in contact with ASN 153 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112C PRO* 3.7 22.5 - - - +
113C SER* 4.9 7.1 + - - +
18D THR 5.9 0.4 + - - -
19D HIS* 5.9 1.4 - - - +
20D PRO* 3.3 31.4 - - + +
21D HIS* 4.3 7.9 - - + +
22D GLU* 4.5 13.8 + - - +
149D ALA 2.8 10.3 + - - -
150D SER 3.5 5.9 + - - -
151D TYR 3.3 2.8 - - - -
152D LEU* 1.3 81.6 - - - +
154D VAL* 1.3 60.2 + - - +
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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