Contacts of the helix formed by residues 159 - 171 (chain B) in PDB entry 3LKB
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 PRO 159 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B TYR* 3.7 29.6 - - + +
127B SER* 3.6 12.5 - - - +
130B VAL* 4.0 20.1 - - + +
150B VAL* 5.7 0.2 - - + -
156B GLY 3.2 15.9 - - - +
158B ALA* 1.3 91.9 - - + +
160B VAL* 1.3 66.4 + - + +
161B GLU 3.4 1.8 - - - -
162B ASP* 3.4 5.8 + - - +
163B ALA* 3.0 21.9 + - - +
205B GLN* 3.7 27.6 - - + +
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Residues in contact with VAL 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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148B LEU* 4.3 20.9 - - + -
150B VAL* 4.3 13.5 - - + -
156B GLY 4.1 6.5 - - - +
157B ARG* 3.1 32.0 + - + +
158B ALA 3.3 0.2 - - - -
159B PRO* 1.3 80.1 - - + +
161B GLU* 1.3 64.2 + - + +
163B ALA* 3.3 8.2 + - - +
164B ARG* 2.8 58.5 + - - +
177B VAL* 4.9 8.7 - - + -
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Residues in contact with GLU 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 ARG 4.7 0.8 + - - -
158B ALA 4.8 1.9 + - - +
159B PRO 3.4 0.6 - - - -
160B VAL* 1.3 82.6 - - + +
162B ASP* 1.3 63.4 + - - +
164B ARG* 3.3 36.0 + - - +
165B LYS* 3.1 34.7 + - - +
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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
----------------------------------------------------------
108B ILE* 4.0 2.1 - - - +
127B SER* 2.8 40.3 + - - +
131B VAL* 4.4 8.5 - - + -
158B ALA 5.4 0.2 - - - +
159B PRO 3.4 3.4 + - - +
160B VAL 3.3 0.4 - - - -
161B GLU* 1.3 73.5 - - - +
163B ALA* 1.3 61.5 + - - +
165B LYS* 3.3 23.3 + - - +
166B ALA* 2.9 31.9 + - - +
378B PHE* 4.6 1.1 - - - -
381B VAL* 3.8 10.7 - - + +
382B HIS* 3.2 41.6 - - - +
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Residues in contact with ALA 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B VAL* 3.7 24.2 - - + +
131B VAL* 4.7 2.3 - - - +
134B LEU* 3.5 16.1 - - + +
148B LEU* 3.9 21.5 - - + -
159B PRO 3.0 13.9 + - - +
160B VAL* 3.3 9.0 - - - +
162B ASP* 1.3 74.0 - - - +
164B ARG* 1.3 66.0 + - - +
166B ALA* 3.4 0.8 + - - -
167B ALA* 3.0 25.3 + - - +
174B ILE* 4.2 3.4 - - + -
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Residues in contact with ARG 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B LEU* 5.7 0.2 - - + -
160B VAL* 2.8 32.6 + - + +
161B GLU* 3.3 33.5 + - - +
163B ALA* 1.3 72.8 - - - +
165B LYS* 1.3 62.9 + - - +
167B ALA* 3.7 2.6 - - - +
168B ARG* 3.2 23.4 + - - +
174B ILE* 4.3 26.2 + - + +
177B VAL* 3.7 36.5 - - - +
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Residues in contact with LYS 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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161B GLU* 3.1 25.0 + - + +
162B ASP* 3.5 22.9 + - - +
164B ARG* 1.3 78.8 - - - +
166B ALA* 1.3 59.4 + - - +
168B ARG* 3.5 10.9 + - + +
169B GLU* 3.1 25.9 + - + +
381B VAL* 2.9 40.7 + - + +
382B HIS* 4.5 4.2 + - - +
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Residues in contact with ALA 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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131B VAL* 4.0 18.2 - - + -
134B LEU* 4.0 12.6 - - + -
162B ASP 2.9 17.5 + - - +
163B ALA 3.7 3.4 - - - +
165B LYS* 1.3 73.1 - - - +
167B ALA* 1.3 67.1 + - - +
169B GLU* 3.2 4.0 + - - +
170B LEU* 3.0 29.4 + - + +
377B LEU* 4.1 16.2 - - + -
381B VAL* 4.1 13.8 - - + +
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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
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134B LEU* 4.1 9.6 - - + +
163B ALA 3.0 18.0 + - - +
164B ARG* 3.7 4.9 - - - +
166B ALA* 1.3 72.8 - - - +
168B ARG* 1.3 67.1 + - - +
170B LEU* 3.0 13.0 + - - -
171B GLY 3.0 11.4 + - - -
172B LEU* 3.1 32.9 + - + +
174B ILE* 3.7 27.4 - - + -
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Residues in contact with ARG 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 ARG 3.2 11.7 + - - +
165B LYS* 3.6 12.8 - - + +
166B ALA 3.3 0.2 - - - -
167B ALA* 1.3 81.3 - - - +
169B GLU* 1.3 87.9 + - + +
170B LEU 3.1 0.7 + - - -
171B GLY* 3.3 9.6 + - - +
172B LEU 4.7 4.0 - - - -
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Residues in contact with GLU 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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165B LYS* 3.1 17.2 + - + +
166B ALA 3.2 8.2 + - - +
168B ARG* 1.3 102.7 + - - +
170B LEU* 1.3 60.6 + - - +
171B GLY 3.5 0.4 + - - -
377B LEU* 4.1 16.1 - - + +
380B LYS* 4.0 23.0 - - - +
381B VAL* 4.0 18.5 - - + +
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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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134B LEU* 3.5 43.5 - - + +
135B GLU* 4.0 10.8 - - + +
138B ALA* 3.9 24.8 - - + +
142B LYS* 5.2 6.6 - - - +
143B GLY 5.0 2.9 + - - -
166B ALA 3.0 19.1 + - - +
167B ALA 3.0 5.8 + - - +
169B GLU* 1.3 77.0 - - - +
171B GLY* 1.3 61.5 + - - +
172B LEU* 3.5 15.4 + - + +
377B LEU* 3.9 26.9 - - + -
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Residues in contact with GLY 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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143B GLY* 3.2 24.2 - - - -
167B ALA 3.0 3.6 + - - -
168B ARG* 3.3 10.1 + - - -
169B GLU 3.5 0.6 - - - -
170B LEU* 1.3 77.8 - - - +
172B LEU* 1.3 62.4 + - - +
173B GLN* 4.0 4.0 + - - +
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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