Contacts of the helix formed by residues 143 - 155 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141B LYS 3.8 1.6 + - - -
142B PHE* 1.4 69.1 - - - +
144B PHE* 1.4 58.1 + - - +
146B HIS* 3.1 7.5 + - - +
147B ILE* 3.0 31.1 + - + +
174B ALA* 3.9 10.3 - - - -
175B VAL 2.9 25.9 + - - +
176B PRO* 3.6 24.5 - - + +
179B MET* 4.4 7.0 - - + -
180B LEU* 3.8 21.0 - - + +
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Residues in contact with PHE 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B GLU* 4.2 17.7 - - + -
110B ALA* 3.6 26.0 - - + -
111B ARG* 3.7 24.5 - - + -
114B VAL* 3.8 31.6 - - + -
142B PHE* 3.3 31.4 - + + -
143B ALA* 1.4 76.3 - - - +
145B VAL* 1.3 56.5 + - + +
147B ILE* 3.9 6.0 - - - +
148B SER* 3.0 29.1 + - - -
175B VAL 4.8 0.9 + - - -
176B PRO* 5.6 0.2 - - - +
179B MET* 3.9 26.0 - - + -
195B LEU* 5.6 3.1 - - + -
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Residues in contact with VAL 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B ALA* 3.9 8.7 - - + -
114B VAL* 3.7 26.9 - - + +
132B PHE* 5.3 0.6 - - - +
135B ALA* 3.4 35.4 - - + +
136B ARG* 3.7 12.6 - - + +
139B CYS* 3.6 30.1 - - + +
142B PHE* 3.1 21.5 + - + +
144B PHE* 1.3 79.4 - - + +
146B HIS* 1.3 63.7 + - + +
148B SER* 3.4 5.4 + - - -
149B PHE* 3.3 20.3 + - - +
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Residues in contact with HIS 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B ARG* 3.4 29.0 + - + +
140B LYS* 2.7 29.2 + - - -
142B PHE 3.2 25.1 - - - -
143B ALA* 3.1 5.9 + - - +
145B VAL* 1.3 77.3 - - + +
147B ILE* 1.3 58.1 + - - +
149B PHE* 3.4 8.3 + - - +
150B ALA* 2.9 28.0 + - - +
165B LEU* 4.5 13.7 + - + +
166B LEU* 4.6 2.4 - - + +
168B LYS* 5.7 0.4 - - - +
169B ALA* 3.6 31.6 + - + +
172B ARG* 6.1 0.2 - - + -
174B ALA* 3.6 15.1 - - + +
180B LEU* 4.6 2.5 - - + -
1199B MLI 3.6 24.9 - - - -
1200B GOL 4.0 5.8 - - - -
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Residues in contact with ILE 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B ALA 3.0 21.0 + - - +
144B PHE* 4.0 5.4 - - - +
145B VAL 3.3 0.2 - - - -
146B HIS* 1.3 73.9 - - - +
148B SER* 1.3 54.4 + - - +
150B ALA* 3.2 1.9 + - - +
151B GLN* 2.7 35.3 + - + +
166B LEU* 3.8 22.9 - - + -
179B MET* 3.5 54.5 - - + +
180B LEU* 3.9 9.6 - - + -
183B ALA* 4.0 3.4 - - + -
194B LEU* 3.8 25.1 - - + +
195B LEU* 4.0 20.0 - - + -
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Residues in contact with SER 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B VAL* 3.4 19.9 - - - +
118B GLU* 2.8 26.8 + - - +
132B PHE* 3.5 18.9 - - - -
144B PHE 3.0 18.3 + - - -
145B VAL 3.5 6.3 - - - -
147B ILE* 1.3 77.0 - - - +
149B PHE* 1.3 56.9 + - - +
151B GLN* 3.4 7.6 + - - +
152B PHE* 3.0 27.7 + - - +
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Residues in contact with PHE 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B ARG* 4.6 4.7 - - + -
132B PHE* 3.5 40.8 - + + +
133B GLN* 3.5 48.5 - - - -
136B ARG* 3.9 17.5 - - + -
145B VAL 3.3 9.6 + - - +
146B HIS* 3.6 10.3 - - - +
148B SER* 1.3 77.9 - - - +
150B ALA* 1.4 58.4 + - - +
152B PHE* 3.2 6.9 + + - +
153B GLU* 3.0 51.8 + - + +
161B LYS* 4.8 7.6 - - - -
165B LEU* 3.7 32.5 - - + -
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Residues in contact with ALA 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146B HIS 2.9 18.4 + - - +
147B ILE 3.5 4.3 - - - +
149B PHE* 1.4 75.8 - - - +
151B GLN* 1.4 55.8 + - - +
153B GLU 3.4 0.3 + - - -
154B LEU* 3.0 18.0 + - - +
162B SER* 2.7 46.3 + - - +
165B LEU* 3.9 13.6 - - + +
166B LEU* 3.7 14.4 - - + -
194B LEU* 3.7 11.2 - - + -
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Residues in contact with GLN 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147B ILE* 2.7 21.7 + - + +
148B SER* 3.5 9.4 - - - +
150B ALA* 1.4 68.5 - - - +
152B PHE* 1.4 61.5 + - - +
154B LEU* 3.4 5.8 + - - +
155B SER* 2.9 36.0 + - - +
192B LYS 3.0 21.8 + - - -
193B GLN* 3.4 23.8 + - - +
194B LEU* 2.8 41.3 + - + +
195B LEU 4.6 0.7 + - - -
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Residues in contact with PHE 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B ALA* 3.9 20.4 - - + -
125B PRO* 3.3 28.9 - - + -
128B ALA* 4.5 1.1 - - + -
129B ARG* 3.9 31.6 - - + -
132B PHE* 3.5 35.7 - + + -
148B SER 3.0 13.8 + - - +
149B PHE* 3.2 10.7 + + - +
151B GLN* 1.4 75.1 - - - +
153B GLU* 1.3 82.2 + - + +
155B SER* 2.7 26.2 + - - -
156B GLN* 3.1 39.1 + - + +
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Residues in contact with GLU 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B ARG* 5.4 3.1 - - - +
149B PHE* 3.0 36.3 + - + +
150B ALA 3.7 7.9 - - - +
152B PHE* 1.3 89.2 - - - +
154B LEU* 1.3 58.3 + - - +
156B GLN* 3.2 9.5 + - - +
157B GLY 3.3 0.2 + - - -
158B ASN* 2.8 73.4 + - - +
161B LYS* 3.8 16.8 - - + +
162B SER* 4.0 9.0 - - - +
165B LEU* 3.7 18.4 - - + -
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Residues in contact with LEU 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150B ALA 3.0 18.3 + - - +
151B GLN* 3.6 6.7 - - - +
153B GLU* 1.3 75.2 - - - +
155B SER* 1.4 57.3 + - - +
157B GLY* 2.9 21.1 + - - -
158B ASN 4.5 3.1 - - - +
159B VAL* 4.1 29.6 - - + +
162B SER* 3.7 10.9 - - - +
187B LEU* 5.1 7.4 - - + -
191B LYS 3.6 19.1 - - - +
192B LYS* 3.5 25.6 - - - +
194B LEU* 4.0 28.7 - - + -
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Residues in contact with SER 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B GLN* 2.9 22.9 + - - +
152B PHE* 2.7 26.3 + - - -
154B LEU* 1.4 75.0 - - - +
156B GLN* 1.4 69.1 + - - +
157B GLY 3.2 0.7 + - - -
192B LYS 6.0 0.2 - - - -
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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
------------------------------------------------------------
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