Contacts of the helix formed by residues 144 - 158 (chain D) in PDB entry 4GKH
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 ASP 144 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222C ILE* 6.0 0.3 - - - +
142D ASN* 2.9 28.3 + - - +
143D SER* 1.3 81.8 - - - +
145D ARG* 1.3 60.6 + - + +
146D VAL* 3.4 13.1 + - - +
147D PHE* 3.0 20.2 + - - +
148D ARG* 2.9 24.4 + - - +
222D ILE* 3.2 9.6 + - + +
223D ALA* 4.5 8.1 - - - +
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Residues in contact with ARG 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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144D ASP* 1.3 73.8 - - - +
146D VAL* 1.3 66.8 + - + +
148D ARG* 4.3 6.7 - - - +
149D LEU* 2.7 44.9 + - + +
186D LEU* 3.4 29.8 - - - +
187D PRO* 3.6 25.1 - - - +
188D PHE* 3.0 48.8 + - + +
190D PRO* 3.8 18.3 - - + +
224D ASP 6.2 0.2 - - - +
263D PHE* 4.0 25.1 - - + -
264D HIS* 5.7 3.1 - - - +
267D LEU* 5.4 2.9 - - + -
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Residues in contact with VAL 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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136C VAL* 5.1 7.9 - - + -
137C CYS* 3.6 27.3 - - + +
144D ASP* 3.3 13.1 + - - +
145D ARG* 1.3 84.5 - - + +
147D PHE* 1.3 62.2 + - - +
149D LEU* 4.1 7.0 - - + +
150D ALA* 3.3 23.4 + - - +
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Residues in contact with PHE 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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137C CYS* 3.1 27.3 - - - +
138C ASN 3.7 11.9 - - - -
139C CYS 3.5 15.7 - - - -
140C PRO* 3.6 35.2 - - + -
71D ARG* 6.2 0.4 - - - -
142D ASN* 3.7 24.7 - - - +
143D SER* 4.4 1.1 - - - -
144D ASP* 3.0 21.6 + - - +
146D VAL* 1.3 80.0 - - - +
148D ARG* 1.3 88.7 + - - +
150D ALA* 3.4 3.5 + - - +
151D GLN* 3.3 52.9 + - + +
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Residues in contact with ARG 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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71D ARG* 5.5 4.4 - - - +
142D ASN 5.1 0.2 + - - -
143D SER* 3.1 48.8 + - - +
144D ASP 2.9 10.8 + - - +
145D ARG* 4.1 2.7 - - - +
147D PHE* 1.3 87.8 - - - +
149D LEU* 1.3 61.2 + - - +
151D GLN* 2.6 45.3 + - - +
152D ALA* 2.9 29.1 + - - +
218D GLY 5.0 1.0 + - - -
219D ARG* 3.2 65.5 + - - +
220D VAL 5.0 0.4 + - - -
227D GLN* 5.8 3.1 - - - +
267D LEU* 3.9 28.0 - - + -
271D PHE* 3.5 3.8 - - + -
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Residues in contact with LEU 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 ARG* 2.7 39.9 + - + +
146D VAL* 4.1 7.4 - - + +
148D ARG* 1.3 72.7 - - - +
150D ALA* 1.3 57.8 + - - +
152D ALA* 3.2 4.3 + - - +
153D GLN* 2.8 30.8 + - - +
179D TRP* 3.6 10.0 - - + -
182D MSE 3.6 31.9 - - + -
183D HIS* 4.2 14.4 - - + +
186D LEU* 4.1 22.9 - - + -
263D PHE* 4.1 18.6 - - + -
267D LEU* 4.0 11.9 - - + -
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Residues in contact with ALA 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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137C CYS* 4.0 29.2 - - + +
146D VAL 3.3 16.0 + - - +
147D PHE 3.7 4.9 - - - +
148D ARG 3.2 0.6 - - - -
149D LEU* 1.3 79.0 - - - +
151D GLN* 1.3 62.1 + - + +
153D GLN* 3.5 12.1 + - - +
154D SER* 3.1 22.2 + - - -
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Residues in contact with GLN 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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147D PHE* 3.3 41.9 + - + +
148D ARG* 2.6 42.9 + - - +
150D ALA* 1.3 74.0 - - + +
152D ALA* 1.3 66.1 + - - +
154D SER* 3.1 7.9 + - - -
155D ARG* 3.0 29.9 + - + +
271D PHE* 3.7 15.5 - - + -
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Residues in contact with ALA 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 ARG 2.9 15.9 + - - +
149D LEU 3.2 5.4 + - - +
151D GLN* 1.3 78.0 - - - +
153D GLN* 1.3 61.7 + - - +
155D ARG* 3.1 5.6 + - - +
156D MSE 2.9 23.7 + - - +
179D TRP* 4.2 7.2 - - + -
267D LEU* 4.1 11.4 - - + -
270D PHE* 3.6 38.0 - - + -
271D PHE* 3.8 12.1 - - + -
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Residues in contact with GLN 153 (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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149D LEU 2.8 15.9 + - - +
150D ALA* 3.7 11.2 - - - +
152D ALA* 1.3 75.8 - - - +
154D SER* 1.3 62.4 + - - +
156D MSE 3.5 11.1 + - + +
157D ASN* 3.1 41.3 + - - +
179D TRP* 3.5 36.3 - - + +
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Residues in contact with SER 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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150D ALA 3.1 14.3 + - - -
151D GLN* 3.1 11.4 + - - -
153D GLN* 1.3 79.4 - - - +
155D ARG* 1.3 56.8 + - - +
157D ASN* 3.4 4.6 + - - +
158D ASN* 2.9 50.4 + - - +
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Residues in contact with ARG 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 GLN* 3.0 14.7 + - + +
152D ALA* 3.1 5.4 + - - +
154D SER* 1.3 74.7 - - - +
156D MSE 1.3 64.0 + - - +
158D ASN* 3.4 2.1 + - - -
159D GLY 3.2 2.6 + - - -
160D LEU* 2.8 82.1 + - + +
161D VAL* 3.8 5.1 + - + +
162D ASP 5.3 0.4 - - - +
270D PHE 2.8 39.9 + - - +
271D PHE* 3.8 36.9 + - - +
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Residues in contact with MSE 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 ALA 2.9 14.5 + - - +
153D GLN* 3.7 14.4 - - + +
155D ARG* 1.3 76.7 - - - +
157D ASN* 1.3 75.7 + - - +
159D GLY* 3.0 20.3 + - - -
161D VAL* 3.7 10.9 - - - +
175D VAL* 3.8 27.1 - - + -
176D GLU* 4.1 24.7 - - + +
179D TRP* 3.7 57.7 - - + +
270D PHE* 4.2 4.5 - - + -
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Residues in contact with ASN 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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153D GLN* 3.1 37.3 + - - +
154D SER* 4.0 5.0 - - - +
156D MSE 1.3 96.8 - - - +
158D ASN* 1.3 63.0 + - - +
159D GLY 3.2 1.5 + - - -
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Residues in contact with ASN 158 (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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154D SER* 2.9 40.5 + - - +
155D ARG* 3.4 0.4 + - - +
156D MSE 3.2 0.4 - - - -
157D ASN* 1.3 80.8 - - - +
159D GLY* 1.3 62.0 + - - +
160D LEU* 3.2 31.9 + - + +
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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