Contacts of the helix formed by residues 155 - 168 (chain B) in PDB entry 4LQL
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 155 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153B ASP* 2.6 8.1 + - + +
154B ALA* 1.3 78.3 - - - +
156B VAL* 1.3 58.5 + - - +
157B GLN 3.1 1.1 - - - -
158B GLU* 3.3 13.4 - - + +
159B GLN* 2.8 34.1 + - - +
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Residues in contact with VAL 156 (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 VAL* 4.0 9.8 - - + +
148B TYR 4.4 6.7 - - - +
149B GLY* 4.2 20.2 - - - +
150B TRP 3.6 20.9 - - - +
151B TRP* 5.2 3.0 - - - -
153B ASP* 2.4 27.7 + - + +
155B ASP* 1.3 71.3 - - - +
157B GLN* 1.3 56.9 + - - +
159B GLN* 4.2 5.8 - - - -
160B ILE* 3.2 28.4 + - - +
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Residues in contact with GLN 157 (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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38B LEU* 3.7 18.2 - - + -
42B GLY* 5.1 13.5 - - - +
44B LEU* 3.9 10.4 - - + +
151B TRP 3.3 26.7 - - - +
152B GLY* 4.2 10.1 - - - +
153B ASP 2.4 24.2 + - - +
154B ALA* 3.2 13.5 - - - +
156B VAL* 1.3 68.5 - - - +
158B GLU* 1.3 57.8 + - - +
160B ILE* 3.8 6.7 + - - -
161B ALA* 3.5 18.9 + - - +
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Residues in contact with GLU 158 (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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154B ALA 2.5 20.4 + - - +
155B ASP* 3.1 18.4 + - + +
157B GLN* 1.3 73.2 - - - +
159B GLN* 1.3 65.3 + - - +
160B ILE 3.1 1.6 - - - -
161B ALA* 3.0 26.0 + - - +
162B ASP* 3.1 25.7 + - - +
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Residues in contact with GLN 159 (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 VAL* 3.8 36.8 - - + +
155B ASP 2.8 23.1 + - - +
156B VAL* 4.1 1.8 - - - +
158B GLU* 1.3 73.5 - - - +
160B ILE* 1.3 61.9 + - - +
162B ASP* 3.8 4.2 + - - +
163B TRP* 3.2 21.0 + - - +
461B GLN* 5.8 1.0 + - - -
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Residues in contact with ILE 160 (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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38B LEU* 5.1 15.5 - - + -
44B LEU* 4.1 20.0 - - + -
77B ILE* 5.3 6.7 - - + -
101B LEU* 4.0 20.4 - - + -
103B LEU* 4.8 11.4 - - + -
147B VAL* 3.8 28.3 - - + -
156B VAL 3.2 23.1 - - - +
157B GLN* 4.1 7.2 - - - +
158B GLU 3.1 0.8 - - - -
159B GLN* 1.3 71.2 - - - +
161B ALA* 1.3 59.6 + - - +
162B ASP 3.1 2.5 - - - -
163B TRP* 4.2 14.6 - - + -
164B GLN* 2.8 35.9 + - + +
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Residues in contact with ALA 161 (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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42B GLY 5.4 1.3 - - - +
43B LYS 4.6 6.5 - - - +
44B LEU* 3.7 27.3 - - + +
45B ASP* 3.7 4.5 - - - +
157B GLN 3.5 12.3 + - - +
158B GLU* 3.0 22.7 + - - +
160B ILE* 1.3 79.1 - - - +
162B ASP* 1.3 61.7 + - - +
164B GLN* 4.6 2.2 - - - -
165B HIS* 3.5 26.0 + - - -
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Residues in contact with ASP 162 (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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158B GLU* 3.1 28.1 + - - +
159B GLN* 4.3 4.5 - - - +
161B ALA* 1.3 80.0 - - - +
163B TRP* 1.3 62.3 + - - +
165B HIS* 3.6 8.0 + - - +
166B VAL* 3.4 19.9 + - - +
458B GLN* 3.9 29.3 - - + +
461B GLN* 5.3 3.1 - - - +
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Residues in contact with TRP 163 (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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9B PHE* 4.6 4.9 - + + -
75B GLY* 4.2 19.7 - - - -
76B VAL 4.3 1.1 - - - -
77B ILE* 3.6 33.7 - - + -
99B PRO* 4.0 21.1 - - - +
100B LEU 4.8 1.0 + - - +
101B LEU* 3.9 37.5 - - + -
145B ALA* 3.9 17.2 - - + +
159B GLN 3.2 18.0 + - - +
160B ILE* 3.1 13.7 + - + +
162B ASP* 1.3 74.9 - - - +
164B GLN* 1.3 81.0 + - + +
165B HIS 3.0 1.6 - - - -
166B VAL* 2.3 33.2 + - + +
167B ALA* 2.9 32.5 + - + +
461B GLN* 3.5 28.7 - - + +
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Residues in contact with GLN 164 (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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9B PHE* 3.6 31.3 - - + -
44B LEU* 4.8 13.0 - - + -
45B ASP* 3.4 23.1 - - - +
46B TYR* 4.4 16.4 - - + +
47B PRO 4.9 1.1 - - - +
48B VAL* 6.2 0.4 - - + -
160B ILE* 2.8 24.2 + - + +
161B ALA* 4.1 1.3 - - - +
163B TRP* 1.3 86.5 - - + +
165B HIS* 1.3 60.1 + - - +
166B VAL 3.1 4.3 + - - -
167B ALA* 3.8 3.5 + - - +
168B VAL* 3.1 25.7 + - - +
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Residues in contact with HIS 165 (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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4B MET* 5.5 5.8 - - + -
45B ASP* 3.1 37.0 - - + -
161B ALA 3.5 13.0 + - - +
162B ASP* 3.8 8.1 - - - +
163B TRP 3.0 0.8 - - - -
164B GLN* 1.3 77.7 - - - +
166B VAL* 1.3 56.9 + - - +
168B VAL* 3.9 16.6 - - - +
169B ALA* 4.8 1.7 + - - +
321B ALA* 4.0 37.7 - - - +
323B ASP 5.7 4.0 - - - -
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Residues in contact with VAL 166 (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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162B ASP 3.4 13.0 + - - +
163B TRP* 2.3 36.3 + - + +
165B HIS* 1.3 68.8 - - - +
167B ALA* 1.3 55.3 + - - +
168B VAL 3.1 5.2 - - - -
169B ALA* 3.8 7.6 + - - +
170B TYR* 4.2 6.6 + - - +
321B ALA* 5.8 5.4 - - + -
454B LEU* 6.5 0.9 - - + -
458B GLN* 3.1 35.0 - - + +
461B GLN* 4.8 7.2 - - - +
462B LEU* 4.0 30.0 - - + +
465B LEU* 5.7 3.1 - - - +
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Residues in contact with ALA 167 (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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9B PHE* 6.1 1.6 - - + -
74B ALA* 3.2 24.5 - - + +
99B PRO* 3.3 30.4 - - + +
163B TRP* 2.9 27.3 + - + +
164B GLN* 3.8 4.9 + - - +
166B VAL* 1.3 73.4 - - - +
168B VAL* 1.3 59.1 + - - +
169B ALA 3.1 6.5 + - - -
170B TYR* 3.7 3.4 + - - +
171B ASN* 3.4 23.9 + - - +
465B LEU* 6.0 1.3 - - - -
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Residues in contact with VAL 168 (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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3B LYS* 6.5 0.9 - - + -
4B MET* 3.8 35.2 - - + -
7B TYR* 4.4 22.8 - - + -
9B PHE* 6.1 1.6 - - + -
46B TYR* 4.5 6.3 - - + -
74B ALA* 4.6 11.4 - - + -
164B GLN 3.1 22.7 - - - +
165B HIS* 3.9 12.6 - - - +
166B VAL 3.1 0.6 - - - -
167B ALA* 1.3 77.9 - - - +
169B ALA* 1.3 58.4 + - + +
171B ASN* 3.7 6.9 - - - +
172B GLU* 3.1 21.0 + - + +
320B ILE* 4.4 20.6 - - + +
321B ALA* 5.8 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