Contacts of the helix formed by residues 163 - 176 (chain B) in PDB entry 1LT8
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 163 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B GLN* 4.7 1.1 - - - +
128B TYR* 3.1 42.6 - + + +
161B PHE* 3.4 1.6 - - - +
162B GLU* 1.3 106.2 - - + +
164B VAL* 1.3 65.7 + - - +
165B GLU 4.3 3.1 - - - +
166B GLU* 4.0 9.8 + - + +
167B ALA* 3.1 22.2 + - - +
185B MET* 3.5 3.6 - - - -
192B ASP* 3.4 5.6 - - - +
193B LEU* 3.4 31.4 - - + +
194B HIS* 3.4 31.2 + + - +
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Residues in contact with VAL 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B HIS* 1.3 71.0 - - - +
165B GLU* 1.3 57.1 + - - +
167B ALA* 3.4 3.3 + - - +
168B VAL* 2.9 40.1 + - + +
185B MET* 3.4 14.5 - - + +
192B ASP* 2.9 21.0 + - + +
196B VAL* 3.6 15.7 - - + -
201B ALA* 3.4 48.5 - - + +
204B ARG* 3.6 32.8 - - + +
205B LEU* 4.9 3.6 - - + -
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Residues in contact with GLU 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B TYR* 2.4 33.1 + - + +
163B HIS* 3.2 0.8 - - - +
164B VAL* 1.3 78.9 - - - +
166B GLU* 1.3 63.4 + - - +
168B VAL* 3.2 10.3 + - - +
169B TRP* 3.2 58.4 + - + +
192B ASP* 4.8 0.6 + - - -
194B HIS* 4.3 11.0 + - - +
204B ARG* 4.3 12.1 - - - +
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Residues in contact with GLU 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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124B GLN* 3.7 20.3 + - - +
125B THR* 2.8 47.4 + - - +
128B TYR* 3.1 45.8 - - + +
137B VAL* 3.9 5.8 - - + +
141B PHE* 4.0 6.5 - - + -
161B PHE* 3.8 11.8 - - + -
163B HIS* 3.3 13.5 + - + +
165B GLU* 1.3 78.0 - - - +
167B ALA* 1.3 66.0 + - - +
169B TRP* 3.5 9.2 + - - +
170B ALA* 3.2 20.8 + - - +
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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
----------------------------------------------------------
158B ALA* 4.7 1.1 - - + +
161B PHE* 3.6 34.9 - - + -
163B HIS 3.1 13.9 + - - +
164B VAL 3.5 9.2 - - - +
166B GLU* 1.3 76.9 - - - +
168B VAL* 1.3 62.9 + - - +
170B ALA* 3.3 4.0 + - - +
171B VAL* 3.1 28.8 + - + +
183B ALA* 5.9 1.1 - - + -
185B MET* 3.6 17.5 - - - -
205B LEU* 4.0 9.6 - - + -
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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
----------------------------------------------------------
164B VAL* 2.9 30.6 + - + +
165B GLU* 3.2 10.3 + - - +
167B ALA* 1.3 74.0 - - - +
169B TRP* 1.3 69.2 + - + +
171B VAL* 3.1 8.6 + - - +
172B GLU* 2.9 48.4 + - - +
204B ARG* 3.5 42.6 - - + +
205B LEU* 4.4 5.4 - - + -
208B ALA* 4.0 13.2 - - + -
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Residues in contact with TRP 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B TYR* 3.7 21.8 - + - -
132B LYS 4.9 0.7 - - - -
133B SER* 4.2 6.5 - - - -
134B GLU* 3.5 44.1 + - + -
137B VAL* 3.2 34.3 - - + -
138B LYS* 3.6 19.0 + - + -
141B PHE* 4.6 2.2 - - + -
165B GLU* 3.2 50.4 + - + +
166B GLU* 3.8 13.5 - - - +
168B VAL* 1.3 81.1 - - + +
170B ALA* 1.3 62.7 + - - +
172B GLU* 3.2 24.7 + - - +
173B THR* 3.0 26.8 + - - -
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Residues in contact with ALA 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B VAL* 4.4 6.7 - - + -
141B PHE* 3.4 33.8 - - + -
158B ALA* 4.3 6.1 - - + -
161B PHE* 3.6 23.3 - - + -
166B GLU 3.2 4.3 + - - +
167B ALA 3.4 9.4 - - - +
168B VAL 3.2 0.2 - - - -
169B TRP* 1.3 78.4 - - - +
171B VAL* 1.3 62.5 + - - +
173B THR* 3.1 4.7 + - - -
174B LEU* 2.9 28.7 + - - +
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Residues in contact with VAL 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B ALA* 4.2 7.0 - - + -
167B ALA 3.1 14.7 + - - +
168B VAL 3.5 7.6 - - - +
170B ALA* 1.3 76.3 - - - +
172B GLU* 1.3 57.8 + - - +
174B LEU* 3.2 8.6 + - - +
175B ILE* 2.9 36.2 + - + +
181B VAL* 4.6 7.2 - - + -
183B ALA* 3.8 28.9 - - + -
205B LEU* 4.1 9.4 - - + +
208B ALA* 3.1 33.2 - - + +
210B ALA* 3.9 18.2 - - + +
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Residues in contact with GLU 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B GLU* 4.0 2.3 - - - +
138B LYS* 3.1 26.6 + - - +
168B VAL* 2.9 39.9 + - + +
169B TRP* 3.2 22.4 + - - +
171B VAL* 1.3 77.4 - - - +
173B THR* 1.3 58.6 + - - +
175B ILE* 3.0 29.5 - - + +
176B ALA* 3.8 7.6 + - - +
208B ALA* 4.3 12.6 - - + +
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Residues in contact with THR 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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138B LYS* 3.7 25.7 + - + +
141B PHE* 4.6 8.0 - - + +
142B LEU* 3.6 44.6 - - + +
145B LEU* 3.1 22.7 - - + +
169B TRP 3.0 13.6 + - - -
170B ALA* 3.1 8.2 + - - -
172B GLU* 1.3 74.5 - - - +
174B LEU* 1.3 66.0 + - - +
176B ALA* 3.3 17.2 + - + +
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Residues in contact with LEU 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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122B VAL* 4.1 30.3 - - + -
141B PHE* 5.3 4.9 - - + +
145B LEU* 4.1 28.0 - - + -
156B LEU* 3.8 18.3 - - + +
157B ILE 4.6 0.4 - - - -
158B ALA* 4.0 24.7 - - + +
170B ALA 2.9 18.1 + - - +
171B VAL 3.2 2.2 + - - +
173B THR* 1.3 78.1 - - - +
175B ILE* 1.3 60.4 + - - +
176B ALA 2.9 6.0 + - - -
177B SER* 2.6 30.3 + - - -
181B VAL* 3.5 34.3 - - + +
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Residues in contact with ILE 175 (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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171B VAL* 2.9 17.1 + - + +
172B GLU* 3.0 27.4 - - + +
174B LEU* 1.3 73.6 - - - +
176B ALA* 1.3 56.9 + - + +
177B SER 2.8 7.3 + - - -
178B GLY* 3.3 12.3 + - - -
179B LYS 4.7 3.4 - - - -
181B VAL* 3.6 15.2 - - + +
208B ALA 3.4 19.7 - - - +
209B GLY* 3.4 34.5 - - - +
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Residues in contact with ALA 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B LEU* 4.7 3.9 - - + +
149B MET* 5.2 1.6 - - - +
172B GLU 3.9 9.6 - - - +
173B THR* 3.3 16.4 + - + +
174B LEU 2.9 2.0 + - - -
175B ILE* 1.3 78.1 - - + +
177B SER* 1.3 57.2 + - - +
178B GLY 3.8 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
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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