Contacts of the helix formed by residues 142 - 157 (chain D) in PDB entry 5JGH
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 142 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140D ASP 3.7 2.6 + - - -
141D LYS* 1.3 77.1 - - - +
143D GLN* 1.3 62.2 + - - +
144D LEU* 4.2 9.9 + - - +
145D ASP* 3.1 25.7 + - - +
146D LEU* 2.8 26.1 + - - +
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Residues in contact with GLN 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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1C T 5.5 2.2 - - - +
131D ARG* 3.3 34.9 + - - -
142D SER* 1.3 74.7 - - - +
144D LEU* 1.3 59.1 + - + +
146D LEU* 3.3 24.8 - - + +
147D MET* 2.8 42.0 + - - +
2E T 5.1 0.2 - - - -
21F A 2.9 33.2 + - - +
22F A 2.5 60.3 + - - +
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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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1C T 4.8 5.4 - - - +
142D SER* 3.2 9.4 - - - +
143D GLN* 1.3 81.0 - - + +
145D ASP* 1.3 63.8 + - - +
147D MET* 3.2 4.3 + - - +
148D LYS* 3.1 26.9 + - + +
1E T 3.6 45.8 - - + +
2E T 3.5 35.9 + - + +
22F A 3.9 19.1 - - + +
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Residues in contact with ASP 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 LYS* 4.0 25.3 + - + +
142D SER* 3.1 25.0 + - - +
144D LEU* 1.3 75.9 - - - +
146D LEU* 1.3 62.3 + - - +
148D LYS* 3.3 22.2 + - - +
149D ILE* 2.8 33.4 + - + +
155G GLN* 3.8 21.7 + - - +
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Residues in contact with LEU 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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131D ARG* 4.7 10.3 - - + +
134D VAL* 3.6 26.5 - - + +
135D PHE* 3.6 45.8 - - + +
138D HIS* 4.2 14.8 - - + +
141D LYS* 4.2 8.5 - - + +
142D SER 2.8 15.5 + - - +
143D GLN* 3.2 31.4 + - + +
145D ASP* 1.3 76.8 - - - +
147D MET* 1.3 52.1 + - + +
149D ILE* 3.1 5.7 + - + +
150D ILE* 2.7 48.6 + - + +
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Residues in contact with MET 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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123D PHE* 4.4 2.9 - - - -
127D ALA* 4.4 19.3 - - + -
128D ASN* 5.3 0.4 - - - +
131D ARG* 3.1 31.4 - - - +
143D GLN* 2.8 30.9 + - + +
144D LEU 3.5 7.0 - - - +
145D ASP 3.2 0.2 - - - -
146D LEU* 1.3 73.2 - - - +
148D LYS* 1.3 56.6 + - - +
150D ILE* 3.3 8.2 + - - +
151D GLY 2.8 25.5 + - - -
2E T 3.1 28.0 - - + +
3E T 3.3 33.1 + - - +
20F A 4.1 13.7 - - + +
21F A 3.6 17.9 - - + +
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Residues in contact with LYS 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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144D LEU* 3.1 13.1 + - + +
145D ASP* 3.3 28.2 + - - +
147D MET* 1.3 74.9 - - - +
149D ILE* 1.3 62.7 + - - +
151D GLY* 3.1 10.0 + - - -
152D ASP* 3.2 9.9 + - - +
2E T 3.2 24.3 + - - +
3E T 3.0 28.6 + - - -
148G LYS 4.9 2.4 + - - -
151G GLY 4.6 0.9 - - - -
152G ASP* 3.2 37.2 + - - +
155G GLN* 4.1 15.9 - - + +
3H T 4.6 9.5 + - - -
4H A 3.2 29.8 + - - -
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Residues in contact with ILE 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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134D VAL* 4.0 17.9 - - + -
138D HIS* 3.9 36.6 - - + +
141D LYS* 4.3 16.2 - - + -
145D ASP 2.8 21.5 + - - +
146D LEU* 3.4 10.5 - - + +
148D LYS* 1.3 73.0 - - - +
150D ILE* 1.3 59.4 + - - +
152D ASP* 3.0 6.2 + - - +
153D LYS* 2.9 35.6 + - + +
152G ASP 4.9 0.2 - - - -
155G GLN* 3.8 32.8 - - + +
156G SER* 3.7 18.8 + - - +
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Residues in contact with ILE 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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123D PHE* 3.8 5.6 - - + -
126D TYR* 3.7 14.8 - - + -
127D ALA* 3.6 31.6 - - + +
130D VAL* 4.0 3.1 - - + -
131D ARG* 3.8 36.8 - - + +
134D VAL* 3.8 26.9 - - + -
146D LEU* 2.7 32.4 + - + +
147D MET* 3.9 14.4 - - - +
149D ILE* 1.3 71.3 - - - +
151D GLY* 1.3 53.5 + - - +
153D LYS* 3.4 7.8 - - + +
154D TRP* 2.7 33.4 + - - +
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Residues in contact with GLY 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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123D PHE* 3.7 13.2 - - - -
147D MET 2.8 13.5 + - - -
148D LYS 3.5 4.5 - - - -
149D ILE 3.1 0.4 - - - -
150D ILE* 1.3 76.3 - - - +
152D ASP* 1.3 57.5 + - - +
154D TRP* 3.0 5.0 + - - +
155D GLN* 2.8 33.7 + - - +
3E T 3.6 20.6 - - - -
4E A 4.1 4.3 + - - +
152G ASP* 5.1 0.4 - - - -
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Residues in contact with ASP 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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148D LYS 3.2 4.0 + - - -
149D ILE 3.0 3.0 + - - +
151D GLY* 1.3 72.4 - - - +
153D LYS* 1.3 67.2 + - - +
155D GLN* 3.3 13.1 + - - +
156D SER* 3.0 36.5 + - - -
149G ILE* 4.8 3.8 - - - +
152G ASP* 4.1 18.3 - - + +
153G LYS* 3.0 37.7 + - - +
156G SER* 3.6 29.7 + - - +
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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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126D TYR* 3.3 22.3 + - - +
130D VAL* 4.5 10.1 - - - +
134D VAL* 3.5 34.1 - - + -
137D GLN* 5.8 1.8 - - - +
149D ILE* 2.9 25.3 + - + +
150D ILE* 3.4 10.1 - - - +
152D ASP* 1.3 76.7 - - - +
154D TRP* 1.3 62.6 + - - +
156D SER* 3.2 6.2 + - - -
157D LEU* 3.0 26.3 + - - +
156G SER* 5.0 2.0 + - - +
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Residues in contact with TRP 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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122D PRO* 3.9 22.7 - - + -
123D PHE* 3.6 20.9 - + + -
126D TYR* 3.5 45.6 - + + -
150D ILE 2.7 16.2 + - - +
151D GLY 3.0 6.0 + - - +
153D LYS* 1.3 72.5 - - - +
155D GLN* 1.3 71.6 + - - +
157D LEU* 3.0 26.0 + - + +
162D LYS* 3.1 53.4 - - + +
165D TYR* 3.9 19.1 - + + -
166D ILE* 4.6 6.3 - - + -
4E A 2.8 37.5 + - - -
5E T 3.1 27.7 + - - -
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Residues in contact with GLN 155 (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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151D GLY 2.8 22.2 + - - +
152D ASP* 3.5 17.7 - - - +
153D LYS 3.3 0.2 - - - -
154D TRP* 1.3 77.2 - - - +
156D SER* 1.3 61.1 + - - +
157D LEU 3.8 1.2 - - - +
162D LYS* 3.3 21.8 + - - +
4E A 2.9 54.3 + - - +
5E T 4.5 3.8 + - - -
138G HIS* 3.2 33.3 - - + +
141G LYS* 5.0 3.8 - - - +
149G ILE* 4.8 10.7 - - + +
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Residues in contact with SER 156 (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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152D ASP* 3.0 27.4 + - - -
153D LYS* 3.7 5.4 - - - -
154D TRP 3.2 0.2 - - - -
155D GLN* 1.3 74.8 - - - +
157D LEU* 1.3 66.9 + - - +
158D ASP* 3.5 5.5 + - - +
153G LYS* 6.0 0.3 + - - -
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Residues in contact with LEU 157 (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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126D TYR* 3.8 34.3 - - + +
153D LYS* 3.0 18.1 + - - +
154D TRP* 3.0 39.1 + - + +
155D GLN 3.8 1.4 - - - +
156D SER* 1.3 79.3 - - - +
158D ASP* 1.3 67.9 + - - +
159D GLN 3.6 0.9 + - - -
161D ILE* 3.7 33.4 - - + -
162D LYS* 3.3 24.4 - - + +
165D TYR* 4.7 0.9 - - + -
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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