Contacts of the helix formed by residues 159 - 171 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126A TYR* 3.8 12.6 - - + +
127A SER* 3.6 34.5 - - - +
130A VAL* 3.9 22.8 - - + +
148A LEU* 5.8 0.2 - - - -
150A VAL* 5.6 0.4 - - + -
156A GLY 3.5 12.3 - - - +
158A ALA* 1.3 95.8 - - + +
160A VAL* 1.3 67.0 + - + +
161A GLU 3.4 1.1 - - - -
162A ASP* 3.3 5.0 + - - +
163A ALA* 3.0 23.1 + - - +
205A GLN* 3.9 20.6 - - + +
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Residues in contact with VAL 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A LEU* 4.4 18.1 - - + +
150A VAL* 4.1 15.9 - - + -
156A GLY 4.0 7.2 - - - +
157A ARG* 3.1 32.0 + - + +
158A ALA 3.3 0.2 - - - -
159A PRO* 1.3 77.5 - - + +
161A GLU* 1.3 68.8 + - + +
163A ALA* 3.2 8.4 + - - +
164A ARG* 3.0 43.1 + - - +
177A VAL* 4.6 19.1 - - + -
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Residues in contact with GLU 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157A ARG 4.7 1.0 + - - -
158A ALA 4.8 2.6 + - - +
159A PRO 3.4 0.6 - - - -
160A VAL* 1.3 82.0 - - + +
162A ASP* 1.3 63.0 + - - +
164A ARG* 3.3 32.5 + - - +
165A LYS* 2.8 43.5 + - + +
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Residues in contact with ASP 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A ILE* 4.1 2.1 - - - +
127A SER* 2.7 39.3 + - - +
131A VAL* 3.9 8.2 - - + +
158A ALA 5.1 2.2 + - - +
159A PRO 3.3 4.6 + - - +
161A GLU* 1.3 77.4 - - - +
163A ALA* 1.3 57.7 + - - +
165A LYS* 3.6 16.8 + - - +
166A ALA* 2.9 30.5 + - - +
378A PHE* 4.7 0.7 - - + -
381A VAL* 3.8 12.0 - - + +
382A HIS* 3.0 46.3 + - - +
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Residues in contact with ALA 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A VAL* 3.7 24.4 - - + +
131A VAL* 4.7 0.9 - - - +
134A LEU* 3.5 16.7 - - + +
148A LEU* 4.0 20.6 - - + -
159A PRO 3.0 14.3 + - - +
160A VAL 3.5 8.7 - - - +
162A ASP* 1.3 75.4 - - - +
164A ARG* 1.3 60.2 + - - +
166A ALA* 4.4 0.7 - - - -
167A ALA* 2.7 33.0 + - - +
174A ILE* 4.9 2.0 - - + -
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Residues in contact with ARG 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A LEU* 5.6 1.3 - - + -
160A VAL* 3.0 26.1 + - + +
161A GLU* 3.3 32.6 + - - +
163A ALA* 1.3 75.2 - - + +
165A LYS* 1.3 66.0 + - - +
167A ALA* 3.2 6.6 + - - +
168A ARG* 3.0 23.7 + - - +
174A ILE* 4.1 27.2 + - + +
177A VAL* 3.2 35.0 - - - +
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Residues in contact with LYS 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A GLU* 2.8 47.0 + - - +
162A ASP* 3.7 12.7 + - - +
164A ARG* 1.3 82.6 - - - +
166A ALA* 1.3 60.1 + - - +
168A ARG* 3.4 14.3 + - - +
169A GLU* 3.1 25.9 + - + +
381A VAL* 3.3 44.1 + - + +
382A HIS* 6.2 0.2 - - - -
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Residues in contact with ALA 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A VAL* 3.8 31.6 - - + -
134A LEU* 4.1 8.1 - - + -
162A ASP 2.9 20.1 + - - +
163A ALA 3.8 3.1 - - - +
165A LYS* 1.3 73.6 - - - +
167A ALA* 1.3 66.1 + - - +
169A GLU* 3.0 12.1 + - - +
170A LEU* 3.0 21.8 + - + +
377A LEU* 4.2 9.6 - - + -
381A VAL* 3.9 11.1 - - + +
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Residues in contact with ALA 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A LEU* 4.2 7.7 - - + +
163A ALA 2.7 21.0 + - - +
164A ARG 3.2 4.7 + - - +
166A ALA* 1.3 69.2 - - - +
168A ARG* 1.3 66.2 + - - +
170A LEU* 3.3 3.3 + - - +
171A GLY 3.0 4.3 + - - -
172A LEU* 2.8 50.8 + - + +
174A ILE* 3.6 29.2 - - + -
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Residues in contact with ARG 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A ARG 3.0 13.0 + - - +
165A LYS* 3.5 17.3 - - - +
167A ALA* 1.3 76.7 - - - +
169A GLU* 1.3 87.2 + - - +
170A LEU 3.1 0.9 + - - -
171A GLY* 3.2 12.2 + - - -
172A LEU 4.8 2.5 - - - -
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Residues in contact with GLU 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A LYS 3.1 15.8 + - - +
166A ALA 3.0 9.1 + - - +
168A ARG* 1.3 99.1 + - + +
170A LEU* 1.3 59.0 + - - +
171A GLY 3.7 0.2 + - - -
377A LEU* 4.1 20.3 - - + +
380A LYS* 5.6 5.7 - - - +
381A VAL* 4.1 15.7 - - + -
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Residues in contact with LEU 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A LEU* 3.7 42.6 - - + +
135A GLU* 3.9 10.5 - - + +
138A ALA* 4.0 19.6 - - + +
142A LYS* 5.8 2.3 - - - +
143A GLY 5.3 1.6 + - - -
166A ALA 3.0 19.6 + - - +
167A ALA 3.9 3.6 - - - +
168A ARG 3.2 0.2 - - - -
169A GLU* 1.3 76.9 - - - +
171A GLY* 1.3 60.0 + - - +
172A LEU* 3.7 17.5 + - + +
377A LEU* 3.6 28.3 - - + -
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Residues in contact with GLY 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A GLY* 3.2 24.8 + - - -
167A ALA 3.0 4.1 + - - -
168A ARG 3.2 9.8 + - - -
169A GLU 3.4 0.6 - - - -
170A LEU* 1.3 79.7 - - - +
172A LEU* 1.3 61.4 + - - +
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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