Contacts of the helix formed by residues 143 - 155 (chain D) in PDB entry 4B94
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 ALA 143 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141D LYS 3.5 3.0 + - - -
142D PHE* 1.3 70.1 - - - +
144D PHE* 1.4 57.5 + - - +
146D HIS* 3.1 6.5 + - - +
147D ILE* 2.9 37.4 + - + +
174D ALA* 3.9 9.6 - - - -
175D VAL 2.9 31.9 + - - +
176D PRO* 3.6 17.5 - - + +
179D MET* 4.4 2.0 - - - -
180D LEU* 3.8 20.9 - - + -
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Residues in contact with PHE 144 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107D GLU* 4.2 19.5 - - + -
110D ALA* 3.6 23.6 - - + -
111D ARG* 3.6 26.9 - - + -
114D VAL* 3.8 32.1 - - + -
142D PHE* 3.2 30.5 - + + -
143D ALA* 1.4 77.7 - - - +
145D VAL* 1.3 56.9 + - + +
147D ILE* 3.9 5.6 - - - +
148D SER* 3.0 29.1 + - - -
176D PRO* 5.5 0.2 - - - +
179D MET* 3.9 24.6 - - + +
195D LEU* 5.9 2.2 - - + -
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Residues in contact with VAL 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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110D ALA* 3.9 19.3 - - + -
114D VAL* 3.8 21.7 - - + +
132D PHE* 5.0 2.1 - - - +
135D ALA* 3.6 40.8 - - + +
136D ARG* 3.6 13.7 - - + +
139D CYS* 3.9 9.6 - - + +
142D PHE* 3.1 28.2 + - + +
144D PHE* 1.3 79.5 - - + +
146D HIS* 1.4 63.6 + - + +
148D SER* 3.4 5.2 + - - -
149D PHE* 3.3 20.6 + - - +
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Residues in contact with HIS 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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136D ARG* 3.4 38.9 + - + +
140D LYS* 2.6 29.9 + - + -
142D PHE 3.2 25.8 - - - -
143D ALA* 3.1 5.3 + - - +
145D VAL* 1.4 79.7 - - + +
147D ILE* 1.4 56.2 + - - +
149D PHE* 3.4 8.0 + - - +
150D ALA* 2.9 27.8 + - - +
165D LEU* 4.5 13.3 + - + +
166D LEU* 4.8 1.3 - - + -
168D LYS* 5.7 0.6 - - - +
169D ALA* 3.6 32.5 + - + +
172D ARG* 6.0 1.3 - - - -
174D ALA* 3.6 13.4 - - + +
180D LEU* 4.6 2.2 - - + -
1201D GOL 3.7 16.4 - - - -
1203D GOL 5.0 2.5 - - - -
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Residues in contact with ILE 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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143D ALA 2.9 20.6 + - - +
144D PHE* 4.0 5.6 - - - +
145D VAL 3.3 0.2 - - - -
146D HIS* 1.4 72.1 - - - +
148D SER* 1.3 55.1 + - - +
150D ALA* 3.2 1.6 + - - +
151D GLN* 2.7 35.7 + - + +
166D LEU* 3.8 23.3 - - + -
179D MET* 3.6 54.5 - - + +
180D LEU* 3.9 10.3 - - + -
183D ALA* 4.1 2.7 - - + -
194D LEU* 4.1 18.6 - - + -
195D LEU* 3.8 26.9 - - + -
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Residues in contact with SER 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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114D VAL* 3.4 19.7 - - - +
118D GLU* 2.9 24.4 + - - +
132D PHE* 3.2 26.4 - - - -
144D PHE 3.0 19.3 + - - -
145D VAL 3.4 6.5 - - - -
146D HIS 3.3 0.2 - - - -
147D ILE* 1.3 73.6 - - - +
149D PHE* 1.3 64.4 + - - +
151D GLN* 3.3 8.0 + - - +
152D PHE* 3.0 19.2 + - - +
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Residues in contact with PHE 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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129D ARG* 4.0 36.8 - - + -
132D PHE* 3.5 40.7 - + + +
133D GLN* 3.6 27.4 - - - -
136D ARG* 4.0 13.2 - - + -
145D VAL 3.3 9.2 + - - +
146D HIS* 3.6 9.6 - - - +
148D SER* 1.3 76.6 - - - +
150D ALA* 1.4 63.5 + - - +
152D PHE* 3.2 7.5 + + - +
153D GLU* 3.0 46.4 + - + +
161D LYS* 4.7 5.2 - - - -
165D LEU* 3.7 31.9 - - + -
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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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146D HIS 2.9 17.4 + - - +
147D ILE 3.2 5.1 + - - +
149D PHE* 1.4 75.1 - - - +
151D GLN* 1.3 55.9 + - - +
153D GLU* 3.4 0.9 + - - -
154D LEU* 3.0 18.9 + - - +
162D SER* 2.7 42.4 + - - +
165D LEU* 3.9 14.7 - - + +
166D LEU* 3.7 13.2 - - + -
194D LEU* 3.6 14.8 - - + -
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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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82A ALA* 5.8 0.2 - - - +
147D ILE* 2.7 22.0 + - + +
148D SER* 3.6 8.3 - - - +
149D PHE 3.3 0.2 - - - -
150D ALA* 1.3 68.5 - - - +
152D PHE* 1.3 61.1 + - - +
154D LEU* 3.4 6.2 + - - +
155D SER* 2.9 36.5 + - - +
192D LYS 3.0 22.6 + - - -
193D GLN* 3.4 24.8 + - - +
194D LEU* 2.8 42.1 + - + +
195D LEU 4.5 1.6 + - - +
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Residues in contact with PHE 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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121D ALA* 3.8 15.7 - - + -
125D PRO* 3.2 30.1 - - + -
128D ALA* 3.9 15.9 - - + -
129D ARG* 3.8 23.3 - - + -
132D PHE* 3.4 40.2 - + + -
148D SER 3.0 7.5 + - - +
149D PHE* 3.2 10.1 + + - +
151D GLN* 1.3 75.7 - - - +
153D GLU* 1.3 81.0 + - - +
155D SER* 2.7 26.6 + - - -
156D GLN* 3.1 40.3 + - + +
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Residues in contact with GLU 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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129D ARG* 3.8 15.4 + - - +
149D PHE* 3.0 34.6 + - + +
150D ALA 3.7 7.4 - - - +
151D GLN 3.3 0.2 - - - -
152D PHE* 1.3 86.2 - - - +
154D LEU* 1.3 59.0 + - - +
156D GLN* 3.2 9.5 + - - +
158D ASN* 2.8 74.1 + - - +
161D LYS* 3.7 23.9 - - + +
162D SER* 4.0 9.2 - - - +
165D LEU* 3.8 9.6 - - + -
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Residues in contact with LEU 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 3.0 16.8 + - - +
151D GLN* 3.6 6.7 - - - +
152D PHE 3.3 0.2 - - - -
153D GLU* 1.3 74.7 - - - +
155D SER* 1.4 56.7 + - - +
157D GLY* 2.9 21.1 + - - -
158D ASN 4.4 2.7 - - - +
159D VAL* 4.0 21.5 - - + +
162D SER* 3.7 8.0 - - - +
187D LEU* 3.6 21.1 - - + -
191D LYS 3.7 18.6 - - - +
192D LYS* 3.5 25.8 - - - +
194D LEU* 3.8 29.2 - - + -
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Residues in contact with SER 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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81A ASP* 4.6 17.2 + - - +
151D GLN* 2.9 21.8 + - - +
152D PHE* 2.7 25.6 + - - -
154D LEU* 1.4 75.2 - - - +
156D GLN* 1.4 68.4 + - - +
157D GLY 3.2 0.8 + - - -
192D LYS 6.0 0.4 - - - -
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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