Contacts of the helix formed by residues 140 - 154 (chain D) in PDB entry 1JPM
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 SER 140 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139D ASN* 1.3 79.2 - - - +
141D PRO* 1.3 75.7 - - - +
142D GLU* 3.8 7.4 + - - +
143D GLU* 3.0 34.2 + - - +
144D MET* 3.0 10.7 + - - +
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Residues in contact with PRO 141 (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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139D ASN 3.6 3.1 - - - +
140D SER* 1.3 86.1 - - - +
142D GLU* 1.3 57.9 + - + +
144D MET* 3.4 3.3 + - + +
145D ALA* 2.9 30.7 + - - +
170D THR* 5.1 3.6 - - + +
173D ALA* 3.7 27.6 - - + +
174D ARG* 3.8 33.9 - - + +
177D GLU* 3.3 17.0 - - + +
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Residues in contact with GLU 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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140D SER* 3.1 7.9 + - - +
141D PRO* 1.3 80.9 - - + +
143D GLU* 1.3 57.5 + - - +
145D ALA* 3.5 0.8 + - - -
146D ALA* 3.0 26.2 + - - +
177D GLU* 4.0 21.1 - - - +
181D ARG* 3.6 15.8 + - - +
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Residues in contact with GLU 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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139D ASN* 3.3 38.2 + - + +
140D SER* 3.0 20.7 + - - +
142D GLU* 1.3 75.2 - - - +
144D MET* 1.3 62.1 + - - +
146D ALA* 3.2 7.8 + - + +
147D ASP* 2.9 42.0 + - - +
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Residues in contact with MET 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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136D VAL* 3.7 26.2 - - + +
137D SER 3.3 24.9 - - - +
138D VAL* 4.1 7.9 - - + -
139D ASN* 3.6 20.2 - - + +
140D SER 3.0 14.6 + - - +
141D PRO* 3.7 4.7 - - + +
143D GLU* 1.3 76.0 - - - +
145D ALA* 1.3 56.0 + - - +
147D ASP* 3.2 5.6 + - - +
148D ALA* 2.8 30.5 + - - +
161D ILE* 3.8 29.4 - - + -
174D ARG* 3.5 38.8 - - + +
178D ILE* 4.0 16.6 - - + -
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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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141D PRO 2.9 19.6 + - - +
142D GLU 3.6 5.2 - - - +
144D MET* 1.3 76.9 - - - +
146D ALA* 1.3 61.3 + - - +
148D ALA* 3.4 2.8 + - - +
149D GLU* 3.1 19.2 + - - +
177D GLU* 3.4 22.9 - - + +
178D ILE* 3.9 11.8 - - - +
181D ARG* 3.3 38.7 - - + +
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Residues in contact with ALA 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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142D GLU 3.0 14.5 + - - +
143D GLU* 3.2 13.4 + - + +
145D ALA* 1.3 78.4 - - - +
147D ASP* 1.3 65.3 + - - +
149D GLU* 3.4 5.3 + - - +
150D ASN* 3.0 22.4 + - - +
181D ARG* 3.4 17.5 - - - +
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Residues in contact with ASP 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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17D LYS* 5.4 3.3 + - - -
136D VAL* 4.1 8.4 - - + +
137D SER* 4.9 7.8 + - - +
139D ASN* 4.7 5.7 - - - +
143D GLU* 2.9 33.4 + - - +
144D MET* 3.2 9.3 + - - +
146D ALA* 1.3 74.7 - - - +
148D ALA* 1.3 59.4 + - - +
150D ASN* 3.0 8.5 + - - +
151D TYR* 2.8 64.6 + - + -
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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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136D VAL* 4.5 4.7 - - + +
144D MET 2.8 19.9 + - - +
145D ALA 3.6 5.4 - - - +
147D ASP* 1.3 74.6 - - - +
149D GLU* 1.3 61.7 + - - +
151D TYR* 3.5 3.0 + - - +
152D LEU* 3.1 24.3 + - - +
159D LEU* 3.6 31.0 - - + +
178D ILE* 3.6 27.4 - - + +
182D VAL* 4.2 7.8 - - + +
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Residues in contact with GLU 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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145D ALA 3.1 9.3 + - - +
146D ALA* 3.6 8.1 - - - +
148D ALA* 1.3 78.3 - - - +
150D ASN* 1.3 63.1 + - - +
152D LEU* 3.3 6.4 - - + +
153D LYS* 3.1 21.8 + - + +
181D ARG* 3.4 32.6 + - + +
182D VAL* 3.7 19.9 - - + +
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Residues in contact with ASN 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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146D ALA 3.0 13.5 + - - +
147D ASP* 3.0 14.3 + - - +
149D GLU* 1.3 75.0 - - - +
151D TYR* 1.3 73.3 + - + +
153D LYS* 2.9 52.8 + - - +
154D GLN* 3.2 19.9 + - - +
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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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17D LYS* 4.2 15.8 + - - -
134D TYR* 3.5 37.0 + + + -
135D THR 3.5 19.0 + - - -
136D VAL* 4.0 19.5 - - + -
137D SER* 5.1 2.8 + - - -
147D ASP* 2.8 51.9 + - + +
148D ALA 4.0 3.4 - - - +
150D ASN* 1.3 78.5 - - + +
152D LEU* 1.3 61.1 + - - +
154D GLN* 3.0 28.9 + - - -
156D PHE* 3.1 32.7 + + + -
159D LEU* 4.0 15.0 - - + -
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Residues in contact with LEU 152 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148D ALA 3.1 13.4 + - - +
149D GLU* 3.3 11.2 - - + +
150D ASN 3.0 0.2 - - - -
151D TYR* 1.3 73.4 - - - +
153D LYS* 1.3 58.9 + - - +
154D GLN 3.0 4.9 - - - -
155D GLY* 2.9 19.2 + - - -
156D PHE 3.6 14.5 + - - +
157D GLN* 4.4 13.0 - - + -
159D LEU* 5.8 0.2 - - + -
182D VAL* 3.4 32.8 - - + -
185D ALA* 4.0 23.1 - - + +
186D VAL* 3.8 18.8 - - + -
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Residues in contact with LYS 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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149D GLU* 3.1 7.8 + - + +
150D ASN* 2.9 47.7 + - - +
152D LEU* 1.3 79.9 - - - +
154D GLN* 1.3 75.2 + - - +
155D GLY 3.3 1.2 + - - -
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Residues in contact with GLN 154 (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 TYR* 6.2 0.2 - - - -
150D ASN* 3.5 25.8 + - - +
151D TYR* 3.0 30.0 + - - +
152D LEU 3.0 1.0 - - - -
153D LYS* 1.3 96.3 - - + +
155D GLY* 1.3 56.5 + - - +
156D PHE* 3.6 16.9 - - + -
341D GLY* 3.6 22.7 - - - -
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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