Contacts of the helix formed by residues 154 - 165 (chain A) in PDB entry 4LQD
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 ASP 154 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93A SER* 5.1 4.6 - - - -
94A GLU* 5.7 2.8 + - - +
150A GLY 3.4 12.9 + - - +
151A PHE 3.3 3.6 + - - +
152A LEU 3.2 1.0 - - - -
153A GLN* 1.3 79.1 - - + +
155A PRO* 1.3 68.2 - - - +
156A TRP* 3.0 23.6 + - - +
157A CME 2.8 53.7 + - - +
158A LYS* 3.3 6.9 + - - +
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Residues in contact with PRO 155 (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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152A LEU 5.0 0.2 - - - -
153A GLN 3.2 11.7 - - - +
154A ASP* 1.3 87.8 - - - +
156A TRP* 1.3 55.3 + - - +
158A LYS* 3.0 16.7 + - + +
159A TYR* 2.9 26.3 + - - +
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Residues in contact with TRP 156 (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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91A CME 5.8 0.8 - - - +
154A ASP* 3.0 15.8 + - - +
155A PRO* 1.3 76.2 - - - +
157A CME 1.3 82.3 + - + +
159A TYR* 3.0 42.0 + + + +
160A GLN* 2.7 59.0 + - + +
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Residues in contact with CME 157 (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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91A CME 3.5 32.9 - - + +
92A HIS 3.7 27.8 - - - -
93A SER* 3.8 17.7 - - - -
94A GLU* 5.0 10.5 + - - +
151A PHE* 3.2 53.2 - - + +
154A ASP* 2.8 38.6 + - - +
156A TRP* 1.3 101.7 + - + +
158A LYS* 1.3 64.8 + - - +
160A GLN* 3.0 8.4 + - + +
161A MET 2.8 19.4 + - - -
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Residues in contact with LYS 158 (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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151A PHE* 4.1 12.1 - - + +
152A LEU* 3.5 42.1 + - + +
154A ASP 3.4 12.8 - - - +
155A PRO* 3.0 14.1 + - + +
157A CME 1.3 74.7 + - - +
159A TYR* 1.3 64.8 + - - +
161A MET* 3.0 22.5 + - - +
162A LEU* 3.1 19.2 + - + +
188A PRO* 6.1 2.0 - - - -
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Residues in contact with TYR 159 (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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155A PRO 2.9 12.4 + - - +
156A TRP* 3.3 49.1 - + + +
158A LYS* 1.3 76.9 - - - +
160A GLN* 1.3 68.1 + - - +
162A LEU* 3.0 25.0 + - + +
163A GLN* 3.0 57.2 + - + +
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Residues in contact with GLN 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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91A CME 3.9 38.6 - - + -
143A ARG* 4.2 11.0 - - - +
145A LEU* 5.3 1.6 - - - -
156A TRP* 2.7 54.1 + - - +
157A CME 3.0 21.3 + - + +
159A TYR* 1.3 77.6 - - - +
161A MET* 1.3 64.2 + - - +
163A GLN* 3.0 15.9 + - - +
164A ALA* 2.9 23.9 + - - +
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Residues in contact with MET 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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145A LEU* 3.6 26.5 - - + -
147A ILE* 4.1 22.4 - - + -
151A PHE* 4.2 12.7 - - + -
157A CME 2.8 11.5 + - - +
158A LYS* 3.0 15.7 + - - +
160A GLN* 1.3 75.8 - - - +
162A LEU* 1.3 68.0 + - + +
164A ALA* 2.9 14.9 + - - +
165A LEU* 3.2 30.8 + - + +
177A PRO* 5.6 1.1 - - + -
188A PRO* 4.5 20.2 - - + -
190A GLU* 4.5 15.5 - - + +
191A LEU* 4.1 26.5 - - + -
194A MET* 5.2 0.2 - - + -
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Residues in contact with LEU 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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158A LYS* 3.1 15.9 + - + +
159A TYR* 3.0 26.3 + - + +
161A MET* 1.3 80.3 - - + +
163A GLN* 1.3 64.6 + - - +
165A LEU* 3.3 16.0 + - + +
166A THR* 3.1 16.8 + - - +
190A GLU* 5.5 7.0 - - - +
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Residues in contact with GLN 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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159A TYR* 3.0 60.2 + - + +
160A GLN* 3.5 19.7 - - - +
162A LEU* 1.3 79.5 - - - +
164A ALA* 1.3 61.9 + - - +
166A THR* 3.2 26.5 + - - +
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Residues in contact with ALA 164 (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 ARG* 3.9 25.6 - - + +
145A LEU* 4.0 9.9 - - + -
160A GLN 2.9 11.3 + - - +
161A MET 2.9 10.0 + - - +
163A GLN* 1.3 78.0 - - - +
165A LEU* 1.3 58.4 + - - +
166A THR 3.3 6.7 + - - +
175A THR* 2.9 40.1 + - + +
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Residues in contact with LEU 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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145A LEU* 5.3 1.1 - - + -
161A MET* 3.2 34.2 + - + +
162A LEU* 3.3 10.7 + - + +
163A GLN 3.2 0.6 - - - -
164A ALA* 1.3 76.7 - - - +
166A THR* 1.3 59.2 + - - +
167A GLU* 4.0 6.7 + - - +
175A THR* 3.7 32.1 - - + +
177A PRO* 5.7 2.7 - - + -
190A GLU* 6.4 0.2 - - + -
194A MET* 3.5 36.3 - - + -
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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