Contacts of the helix formed by residues 162 - 174 (chain B) in PDB entry 3L2U
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 SER 162 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160B ALA* 2.9 17.9 + - - +
161B PRO* 1.3 77.8 - - - +
163B THR* 1.3 65.6 + - - +
164B SER* 3.5 10.0 + - - -
165B ALA* 3.2 21.1 + - - +
166B THR* 2.9 23.6 + - - -
189B ALA* 3.7 4.5 - - - -
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Residues in contact with THR 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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162B SER* 1.3 71.7 - - - +
164B SER* 1.3 66.1 + - - +
166B THR* 3.0 6.7 + - - -
167B VAL* 2.8 30.3 + - + +
189B ALA* 3.0 22.2 + - - +
192B SER* 2.9 35.4 + - - +
194B THR* 4.1 13.9 - - + -
195B PHE* 3.8 23.3 - - + +
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Residues in contact with SER 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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162B SER* 3.2 8.8 + - - -
163B THR* 1.3 81.2 - - - +
165B ALA* 1.3 62.7 + - - +
167B VAL* 3.2 5.5 + - - +
168B LYS* 3.0 23.3 + - - +
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Residues in contact with ALA 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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129B TYR* 3.7 2.7 - - - +
158B THR* 3.7 18.3 - - - +
159B LYS 4.9 1.6 - - - +
160B ALA* 3.3 30.3 - - + +
162B SER* 3.2 11.0 + - - +
164B SER* 1.3 76.1 + - - +
166B THR* 1.3 65.4 + - - +
168B LYS* 3.4 6.7 + - - +
169B SER* 3.0 27.9 + - - -
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Residues in contact with THR 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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127B ILE* 4.7 1.1 - - + -
129B TYR* 3.0 24.7 + - - -
143B LEU* 4.3 11.0 - - + -
162B SER 2.9 15.1 + - - -
163B THR* 3.0 10.7 + - - -
165B ALA* 1.3 74.5 - - - +
167B VAL* 1.3 59.5 + - - +
169B SER* 3.2 1.9 + - - -
170B LEU* 2.8 42.4 + - + +
189B ALA* 4.3 2.0 - - - +
190B PHE* 4.2 17.6 - - + -
195B PHE* 3.6 31.4 - - + -
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Residues in contact with VAL 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B THR* 2.8 28.3 + - + +
164B SER* 3.7 5.8 - - - +
166B THR* 1.3 77.8 - - - +
168B LYS* 1.3 65.3 + - - +
170B LEU* 3.7 2.6 - - - +
171B ASN* 2.8 36.9 + - - +
194B THR* 5.5 4.3 - - + -
195B PHE* 4.0 22.4 - - + -
198B TRP* 3.4 39.0 - - + +
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Residues in contact with LYS 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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164B SER 3.0 13.1 + - - +
165B ALA* 3.8 9.2 - - - +
167B VAL* 1.3 77.3 - - - +
169B SER* 1.3 63.7 + - - +
171B ASN* 3.3 11.0 + - - +
172B VAL* 3.3 21.8 + - - +
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Residues in contact with SER 169 (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 LEU* 3.7 19.3 - - - -
156B TYR* 3.6 26.8 - - - +
157B PRO 4.6 2.3 + - - -
158B THR* 3.6 18.9 - - - +
165B ALA 3.0 18.1 + - - -
166B THR 3.6 3.4 - - - -
168B LYS* 1.3 76.8 - - - +
170B LEU* 1.3 58.6 + - - +
172B VAL* 3.0 29.9 + - - +
173B LEU 3.2 5.0 + - - -
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Residues in contact with LEU 170 (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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125B PHE* 6.2 0.9 - - + -
127B ILE* 4.5 12.3 - - + -
143B LEU* 3.9 18.2 - - + -
145B VAL* 4.2 17.7 - - + -
156B TYR* 5.3 1.1 - - + -
166B THR* 2.8 30.2 + - + +
167B VAL* 4.1 0.7 - - - +
169B SER* 1.3 71.2 - - - +
171B ASN* 1.3 54.0 + - - +
173B LEU* 3.7 14.9 - - + +
174B THR* 2.6 44.0 + - + +
182B ILE* 4.0 17.0 - - + -
195B PHE* 3.9 23.1 - - + -
198B TRP* 3.7 30.7 - - + -
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Residues in contact with ASN 171 (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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247A PRO* 5.1 6.4 - - + +
167B VAL* 2.8 35.1 + - - +
168B LYS* 3.5 9.8 - - - +
170B LEU* 1.3 77.3 - - - +
172B VAL* 1.3 63.6 + - + +
174B THR* 3.4 11.8 + - - -
175B SER* 3.2 15.9 + - - -
198B TRP* 3.0 22.8 + - - -
202B ARG* 3.3 17.1 + - - +
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Residues in contact with VAL 172 (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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172A VAL* 5.8 8.1 - - + -
156B TYR* 3.4 28.0 - - + +
168B LYS 3.3 10.7 + - - +
169B SER* 3.0 13.7 + - - +
171B ASN* 1.3 81.9 - - + +
173B LEU* 1.3 61.3 + - - +
174B THR 3.3 0.2 + - - -
175B SER* 3.3 17.6 + - - -
176B ILE* 4.2 6.8 - - + +
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Residues in contact with LEU 173 (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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125B PHE* 3.6 23.1 - - + -
145B VAL* 3.5 40.6 - - + -
154B TRP* 3.5 36.8 - - + +
156B TYR* 3.2 27.6 - - + +
169B SER 3.2 5.2 + - - +
170B LEU* 3.2 15.5 + - + +
172B VAL* 1.3 78.5 - - - +
174B THR* 1.3 62.1 + - + +
175B SER 3.1 0.2 - - - -
176B ILE* 3.1 30.6 + - + +
177B ALA* 3.4 11.2 + - + +
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Residues in contact with THR 174 (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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251A LEU* 3.6 19.9 - - - +
125B PHE* 6.0 0.4 - - + -
170B LEU* 2.6 28.5 + - + +
171B ASN* 3.4 10.4 + - - -
172B VAL 3.2 0.4 - - - -
173B LEU* 1.3 81.1 - - + +
175B SER* 1.3 58.3 + - - +
176B ILE 3.3 0.7 - - - -
177B ALA 3.4 21.3 - - - +
178B ILE* 4.0 13.6 - - + +
179B PRO* 4.1 17.3 - - + -
182B ILE* 6.3 0.2 - - + -
198B TRP* 4.2 20.1 - - + -
202B ARG* 4.6 7.4 + - - -
204B ILE* 4.9 2.7 - - + -
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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