Contacts of the helix formed by residues 140 - 154 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139A ASN* 1.3 79.1 - - - +
141A PRO* 1.3 75.4 - - - +
142A GLU* 2.9 11.0 + - - +
143A GLU* 3.4 21.5 + - - +
144A MET* 3.1 16.3 + - - +
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Residues in contact with PRO 141 (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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139A ASN 3.5 2.6 - - - +
140A SER* 1.3 85.9 - - - +
142A GLU* 1.3 56.7 + - + +
144A MET* 3.6 4.3 + - + +
145A ALA 3.1 19.2 + - - -
170A THR* 6.1 2.5 - - + -
173A ALA* 3.6 33.2 - - + +
174A ARG* 3.6 25.5 - - + +
177A GLU* 3.0 27.3 - - + +
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Residues in contact with GLU 142 (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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140A SER* 2.9 9.6 + - - +
141A PRO* 1.3 81.3 - - + +
143A GLU* 1.3 65.1 + - + +
145A ALA* 3.3 3.5 + - - +
146A ALA* 3.2 20.3 + - - +
177A GLU* 4.0 11.9 - - - +
181A ARG* 3.7 23.0 + - - -
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Residues in contact with GLU 143 (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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139A ASN* 3.2 37.5 + - + +
140A SER* 3.1 17.3 + - - +
142A GLU* 1.3 78.8 - - + +
144A MET* 1.3 60.3 + - - +
146A ALA* 3.1 8.9 + - + +
147A ASP* 2.9 40.8 + - - +
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Residues in contact with MET 144 (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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136A VAL* 3.7 26.9 - - + +
137A SER 3.4 24.9 - - - +
138A VAL* 4.1 9.9 - - + -
139A ASN* 3.4 27.8 - - + +
140A SER 3.1 14.7 + - - +
141A PRO* 3.8 5.4 - - + +
143A GLU* 1.3 76.2 - - - +
145A ALA* 1.3 57.2 + - - +
147A ASP* 3.4 2.6 + - - -
148A ALA* 2.9 31.2 + - - +
161A ILE* 4.0 26.9 - - + -
162A LYS 5.5 0.2 - - - +
174A ARG* 3.5 31.4 - - + +
178A ILE* 4.1 17.3 - - + -
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Residues in contact with ALA 145 (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 PRO 3.1 19.0 + - - +
142A GLU 3.5 5.2 - - - +
143A GLU 3.2 0.2 - - - -
144A MET* 1.3 75.8 - - - +
146A ALA* 1.3 61.4 + - - +
148A ALA* 3.7 2.8 + - - +
149A GLU* 3.3 20.6 + - - +
177A GLU* 3.5 33.4 - - + +
178A ILE* 4.1 11.8 - - - +
181A ARG* 3.6 26.9 - - + +
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Residues in contact with ALA 146 (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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142A GLU* 3.2 11.8 + - - +
143A GLU* 3.1 13.6 + - + +
145A ALA* 1.3 75.5 - - - +
147A ASP* 1.3 67.9 + - - +
149A GLU* 2.9 15.8 + - - +
150A ASN* 3.1 21.4 + - - +
181A ARG* 3.3 23.7 - - - +
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Residues in contact with ASP 147 (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 LYS* 4.9 6.0 + - - -
136A VAL* 4.3 6.5 - - + +
137A SER* 4.9 6.2 + - - +
139A ASN* 4.7 6.4 + - - -
143A GLU* 2.9 36.8 + - - +
144A MET* 3.9 4.9 - - - +
146A ALA* 1.3 75.8 - - - +
148A ALA* 1.3 63.3 + - - +
150A ASN* 3.0 16.0 + - - +
151A TYR* 2.8 59.8 + - + -
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Residues in contact with ALA 148 (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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136A VAL* 4.5 4.9 - - + +
144A MET 2.9 18.4 + - - +
145A ALA 3.7 5.8 - - - +
147A ASP* 1.3 76.3 - - - +
149A GLU* 1.3 57.4 + - - +
151A TYR* 3.6 5.6 + - - +
152A LEU* 3.0 29.6 + - - +
159A LEU* 3.7 29.5 - - + +
178A ILE* 3.7 23.6 - - + -
182A VAL* 4.0 7.5 - - + +
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Residues in contact with GLU 149 (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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145A ALA 3.3 9.4 + - - +
146A ALA* 2.9 10.6 + - - +
148A ALA* 1.3 77.7 - - - +
150A ASN* 1.3 62.9 + - - +
152A LEU* 3.3 6.2 + - + +
153A LYS* 2.9 29.1 + - + +
181A ARG* 3.1 39.5 + - - +
182A VAL* 4.0 15.2 - - + +
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Residues in contact with ASN 150 (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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146A ALA* 3.1 27.5 + - - +
147A ASP* 3.0 16.9 + - - +
149A GLU* 1.3 79.4 - - - +
151A TYR* 1.3 71.3 + - + +
153A LYS* 3.0 10.1 + - - +
154A GLN* 2.9 31.0 + - + +
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Residues in contact with TYR 151 (chain A).
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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17A LYS* 3.3 26.2 + - - -
134A TYR* 3.4 42.2 + + + -
135A THR 3.6 11.1 + - - -
136A VAL* 4.0 21.3 - - + -
137A SER 4.9 0.9 + - - -
147A ASP* 2.8 50.7 + - + +
148A ALA* 3.8 4.5 - - - +
150A ASN* 1.3 76.0 - - + +
152A LEU* 1.3 58.0 + - - +
154A GLN* 2.9 34.1 + - - -
156A PHE* 3.1 29.2 + + + -
159A LEU* 4.0 15.5 - - + -
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Residues in contact with LEU 152 (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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148A ALA 3.0 18.1 + - - +
149A GLU* 3.5 7.0 - - + +
150A ASN 3.2 0.2 - - - -
151A TYR* 1.3 75.7 - - - +
153A LYS* 1.3 58.1 + - - +
155A GLY* 3.0 19.8 + - - -
156A PHE 3.4 13.9 + - - +
157A GLN* 4.2 13.4 - - + +
182A VAL* 3.7 30.7 - - + -
185A ALA* 3.8 20.4 - - + +
186A VAL* 3.4 25.8 - - + -
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Residues in contact with LYS 153 (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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149A GLU* 2.9 15.2 + - + +
150A ASN* 3.0 13.7 + - - +
152A LEU* 1.3 76.2 - - - +
154A GLN* 1.3 59.7 + - + +
155A GLY 3.3 0.6 + - - -
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Residues in contact with GLN 154 (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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134A TYR* 5.9 1.2 - - - -
150A ASN* 2.9 16.8 + - + +
151A TYR* 2.9 33.3 + - - +
153A LYS* 1.3 81.7 - - + +
155A GLY* 1.3 56.9 + - - +
156A PHE* 3.6 17.9 - - + -
341A GLY* 3.6 20.4 - - - -
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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