Contacts of the helix formed by residues 152 - 163 (chain B) in PDB entry 3LQ5
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 HIS 152 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57B LEU* 3.5 28.5 - - + -
60B ASN* 3.2 43.1 - - + +
61B THR* 3.0 25.7 + - - -
64B VAL* 3.5 19.5 - - + +
95B GLU* 5.4 0.9 - - - -
150B ILE* 3.6 17.3 - - + +
151B ASP* 1.3 77.8 + - - +
153B PRO* 1.3 74.8 - - + +
154B HIS* 2.9 17.4 + - + +
155B THR* 3.1 20.0 + - - +
156B HIS* 3.7 6.8 + - - -
182B LEU* 4.2 7.5 - - - +
193B PRO* 4.0 3.4 - - - -
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Residues in contact with PRO 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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151B ASP 4.5 1.8 - - - +
152B HIS* 1.3 91.4 - - + +
154B HIS* 1.3 75.1 + - + +
156B HIS* 2.9 18.0 + - - +
157B VAL* 3.1 12.0 + - + +
178B ALA* 4.5 9.4 - - + +
181B SER* 4.9 4.7 - - - +
182B LEU* 5.3 8.7 - - + -
188B SER* 6.5 1.1 - - - -
193B PRO* 3.7 29.0 - - + +
196B VAL* 3.5 33.7 - - + -
197B ALA* 3.8 8.8 - - - +
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Residues in contact with HIS 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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56B GLN* 5.7 2.0 - - + -
57B LEU* 5.9 4.7 - - + -
60B ASN* 3.3 27.2 + - - -
152B HIS* 2.9 13.4 + - + +
153B PRO* 1.3 79.8 - - + +
155B THR* 1.3 65.0 + - - +
157B VAL* 3.0 24.5 + - - +
158B VAL* 3.7 4.5 + - - +
175B TYR* 3.8 32.3 + + + -
178B ALA* 3.4 26.0 - - + +
179B THR* 2.9 36.9 + - - -
182B LEU* 4.3 7.0 - - + -
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Residues in contact with THR 155 (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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151B ASP* 3.7 10.4 + - - +
152B HIS* 3.1 14.1 + - - +
153B PRO 3.0 0.6 + - - -
154B HIS* 1.3 78.1 - - - +
156B HIS* 1.3 75.1 + - + +
157B VAL 3.2 0.3 + - - -
158B VAL* 3.5 20.1 + - - +
159B LYS* 3.9 24.3 + - - +
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Residues in contact with HIS 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B ASP* 3.3 34.6 + - - -
152B HIS 3.7 7.2 + - - -
153B PRO 2.9 7.0 + - - +
155B THR* 1.3 81.4 - - + +
157B VAL* 1.3 67.0 + - - +
159B LYS* 3.2 27.8 + - + +
160B CYS* 3.1 26.4 + - - -
193B PRO* 4.0 8.5 - - + +
194B PRO* 3.6 35.7 - - + +
197B ALA* 3.7 14.6 - - + -
225B VAL* 5.2 6.3 - - + -
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Residues in contact with VAL 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B PRO 3.1 14.8 + - - +
154B HIS* 3.0 18.4 + - - +
156B HIS* 1.3 75.8 - - - +
158B VAL* 1.3 67.9 + - - +
160B CYS* 3.0 12.6 + - - +
161B THR* 3.1 21.1 + - + +
174B SER* 4.0 22.4 - - - +
175B TYR* 3.5 34.1 - - + -
178B ALA* 4.5 15.3 - - + -
197B ALA* 4.3 12.3 - - + +
200B CYS* 5.1 1.1 - - + -
201B ILE* 4.3 13.7 - - + -
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Residues in contact with VAL 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 HIS 4.2 2.9 - - - +
155B THR* 3.6 13.7 - - - +
157B VAL* 1.3 75.9 - - - +
159B LYS* 1.3 67.2 + - + +
161B THR* 2.7 24.4 + - - +
162B GLN* 3.1 31.5 + - + +
175B TYR* 2.8 26.5 + - + +
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Residues in contact with LYS 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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155B THR* 3.9 24.5 + - - +
156B HIS* 3.5 44.0 - - + +
157B VAL 3.1 0.8 + - - -
158B VAL* 1.3 78.3 - - + +
160B CYS* 1.3 65.1 + - - +
161B THR 3.1 1.4 + - - -
162B GLN* 3.3 21.6 + - - +
163B LEU* 3.3 21.8 + - + +
225B VAL* 5.7 5.8 - - + -
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Residues in contact with CYS 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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156B HIS 3.1 16.6 + - - -
157B VAL 3.0 3.3 + - - +
159B LYS* 1.3 78.0 - - - +
161B THR* 1.3 58.5 + - - +
162B GLN 3.5 0.2 - - - -
163B LEU* 3.5 14.5 + - - +
164B VAL* 3.5 23.2 - - - +
197B ALA* 4.6 5.6 - - - -
198B CYS* 4.6 4.7 - - - -
201B ILE* 3.5 34.3 - - + +
221B TRP* 4.4 17.2 - - + -
225B VAL* 3.7 36.3 - - - -
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Residues in contact with THR 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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157B VAL* 3.3 23.6 + - + +
158B VAL* 2.7 23.0 + - - -
159B LYS 3.0 0.2 - - - -
160B CYS* 1.3 81.3 - - - +
162B GLN* 1.3 62.9 + - - +
163B LEU 3.2 0.4 - - - -
164B VAL* 3.5 2.9 + - - +
165B ARG* 3.3 3.1 + - - -
166B ALA* 3.2 39.6 + - + +
170B LEU* 5.6 2.2 - - + -
171B ALA* 4.6 20.4 - - - +
174B SER* 4.5 7.0 - - - +
175B TYR* 5.5 0.9 + - - -
201B ILE* 4.1 19.1 - - + -
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Residues in contact with GLN 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 VAL* 3.1 33.9 + - + +
159B LYS* 3.7 12.9 - - - +
161B THR* 1.3 76.0 - - - +
163B LEU* 1.3 65.9 + - + +
164B VAL 3.0 6.2 + - - -
165B ARG* 3.2 25.7 + - - +
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Residues in contact with LEU 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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159B LYS* 3.3 19.7 + - + +
160B CYS* 3.7 8.3 - - - +
161B THR 3.2 1.2 - - - -
162B GLN* 1.3 84.1 - - + +
164B VAL* 1.3 67.3 + - + +
165B ARG* 5.7 3.1 - - - +
221B TRP* 3.9 22.3 - - + +
224B TYR* 3.6 40.4 - - + +
225B VAL* 4.3 12.3 - - + -
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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