Contacts of the helix formed by residues 142 - 156 (chain A) in PDB entry 4G98
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138A LEU 2.8 20.7 + - - -
139A GLY 3.1 1.3 + - - -
141A LEU* 1.3 74.7 - - - +
143A GLY* 1.3 63.6 + - - -
144A GLY 3.2 0.7 - - - -
145A GLN* 3.0 27.9 + - - +
146A VAL* 4.0 4.8 + - - +
179A LYS* 3.8 24.2 + - - +
301A HEM 3.5 38.6 + - - +
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Residues in contact with GLY 143 (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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139A GLY 3.2 1.8 + - - -
142A SER* 1.3 76.7 - - - +
144A GLY* 1.3 64.9 + - - +
145A GLN 3.0 2.2 - - - -
146A VAL* 3.0 13.8 + - - +
147A LEU* 3.0 26.8 + - - +
301A HEM 3.5 28.7 + - - +
302A CMO 3.4 13.6 + - - -
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Residues in contact with GLY 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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139A GLY 3.0 12.1 + - - -
140A ASP* 3.6 16.6 - - - -
142A SER 3.2 0.2 - - - -
143A GLY* 1.3 76.6 - - - +
145A GLN* 1.3 62.6 + - - +
147A LEU* 3.3 11.2 + - - +
148A LYS* 2.9 24.4 + - - +
166A PHE* 6.4 0.7 - - - -
167A PHE* 3.3 19.8 - - - -
302A CMO 3.1 4.5 + - - -
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Residues in contact with GLN 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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140A ASP 3.4 19.2 - - - +
141A LEU* 4.0 11.7 - - - +
142A SER 3.0 13.6 + - - +
143A GLY 3.0 0.8 - - - -
144A GLY* 1.3 77.0 - - - +
146A VAL* 1.3 65.3 + - + +
148A LYS* 3.4 28.4 - - - +
149A LYS* 3.4 26.3 + - - +
167A PHE* 3.1 28.9 + - - +
169A PHE* 3.8 11.6 - - - -
175A PRO* 5.0 15.0 - - + +
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Residues in contact with VAL 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 SER 4.5 3.8 - - - +
143A GLY* 3.0 19.1 + - - +
145A GLN* 1.3 76.3 - - + +
147A LEU* 1.3 64.9 + - - +
149A LYS* 3.2 28.3 + - - +
150A ILE* 3.2 29.2 + - + +
301A HEM 4.8 25.1 - - + -
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Residues in contact with LEU 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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34A MET* 4.6 11.2 - - - -
37A PHE* 3.6 32.0 - - + -
38A GLN* 4.8 1.6 - - + -
143A GLY 3.0 16.8 + - - +
144A GLY* 3.6 14.4 - - - +
146A VAL* 1.3 75.7 - - - +
148A LYS* 1.3 63.1 + - - +
150A ILE* 3.2 12.0 + - + -
151A ALA* 2.9 24.6 + - - +
167A PHE* 4.3 12.1 - - + -
301A HEM 4.0 53.4 - - + -
302A CMO 4.8 2.5 - - - +
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Residues in contact with LYS 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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144A GLY 2.9 13.6 + - - +
145A GLN* 3.4 23.2 - - - +
147A LEU* 1.3 74.5 - - - +
149A LYS* 1.3 60.1 + - + +
151A ALA* 3.2 7.3 + - - +
152A GLN* 2.9 45.5 + - - +
161A GLY* 5.8 5.2 - - - -
164A LEU* 4.1 18.8 - - + +
167A PHE* 3.7 39.5 + - + +
168A THR* 3.0 31.7 + - - +
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Residues in contact with LYS 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 GLN* 3.4 28.4 + - - +
146A VAL* 3.2 20.1 + - - +
148A LYS* 1.3 82.0 - - + +
150A ILE* 1.3 65.9 + - + +
152A GLN* 3.3 12.2 + - - +
153A LYS* 3.1 25.1 + - - +
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Residues in contact with ILE 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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37A PHE* 3.2 33.4 - - + +
38A GLN* 3.7 29.8 - - + +
40A GLY* 3.9 17.4 - - - +
42A VAL* 5.9 0.7 - - + -
146A VAL* 3.2 30.7 + - + +
147A LEU* 3.2 16.4 + - + +
149A LYS* 1.3 78.1 - - + +
151A ALA* 1.3 64.4 + - - +
153A LYS* 3.3 7.3 + - - +
154A ALA* 2.9 27.9 + - + +
301A HEM 5.9 0.2 - - + -
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Residues in contact with ALA 151 (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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37A PHE* 4.0 10.7 - - + -
42A VAL* 4.9 1.8 - - - -
47A PHE* 4.0 27.4 - - + -
147A LEU 2.9 16.1 + - - +
148A LYS* 3.6 5.8 - - - +
150A ILE* 1.3 76.9 - - - +
152A GLN* 1.3 63.3 + - - +
154A ALA* 4.5 2.7 - - - -
155A MET* 2.9 40.3 + - + +
157A LEU* 4.1 1.3 - - - +
164A LEU* 4.2 11.9 - - + -
167A PHE* 5.6 0.7 - - + -
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Residues in contact with GLN 152 (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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148A LYS* 2.9 32.2 + - - +
149A LYS* 3.4 13.1 - - - +
151A ALA* 1.3 77.9 - - - +
153A LYS* 1.3 57.3 + - - +
156A ALA* 3.1 10.2 + - - -
157A LEU* 3.0 53.7 + - - +
158A PRO 4.4 4.7 - - - +
159A SER* 3.7 29.8 + - - +
164A LEU* 3.9 21.2 - - + +
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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 LYS 3.1 16.1 + - - +
150A ILE* 3.8 5.6 - - - +
152A GLN* 1.3 75.8 - - + +
154A ALA* 1.3 69.1 + - - +
155A MET 3.4 0.3 + - - -
156A ALA* 3.7 5.9 + - - +
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Residues in contact with ALA 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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40A GLY* 3.5 32.3 - - - +
42A VAL* 4.3 21.1 - - + +
150A ILE* 2.9 18.2 + - + +
151A ALA 3.8 2.7 - - - +
153A LYS* 1.3 82.6 - - - +
155A MET* 1.3 60.9 + - - +
156A ALA* 3.8 0.5 + - - +
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Residues in contact with MET 155 (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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42A VAL* 4.1 17.9 - - + +
43A SER 4.2 2.5 - - - +
44A ARG* 4.1 23.6 - - + +
47A PHE* 3.8 41.3 - - + -
96A TRP* 4.3 11.1 - - + -
151A ALA* 2.9 34.5 + - + +
154A ALA* 1.3 80.6 - - + +
156A ALA* 1.3 70.6 + - - +
157A LEU* 3.4 25.5 - - + +
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Residues in contact with ALA 156 (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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152A GLN 3.1 8.4 + - - -
153A LYS 3.7 4.9 + - - +
154A ALA 3.5 3.0 - - - +
155A MET* 1.3 81.2 - - - +
157A LEU* 1.3 62.2 + - - +
158A PRO* 3.8 3.6 - - - +
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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