Contacts of the strand formed by residues 159 - 166 (chain A) in PDB entry 4LML
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 TRP 159 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A LEU* 3.5 40.3 + - + +
31A ASP* 4.3 3.1 + - - -
113A LEU* 5.4 2.2 - - + -
121A ASP* 4.5 1.8 - - - -
123A GLN* 4.0 21.8 - - + -
155A PHE 3.9 8.5 - - - +
156A LEU* 2.9 36.3 + - + +
157A THR 3.6 12.3 - - - -
158A GLY* 1.3 97.6 + - - +
160A ASP* 1.3 61.6 + - - +
161A ILE* 4.1 1.3 + - - +
189A ILE* 3.4 27.6 - - + -
190A SER* 3.6 8.5 - - - -
191A ARG* 3.1 77.5 - - + +
192A GLN* 3.1 18.0 + - - -
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Residues in contact with ASP 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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159A TRP* 1.3 72.2 - - - +
161A ILE* 1.3 62.3 + - - +
162A GLU* 3.5 9.5 - - - +
189A ILE* 3.3 6.9 - - - +
190A SER* 2.9 53.4 + - - +
191A ARG 4.8 1.2 - - - +
192A GLN* 2.7 41.1 + - - +
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Residues in contact with ILE 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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23A LEU* 5.8 0.7 - - + -
26A CYS* 4.8 8.5 - - + -
150A LYS* 3.4 33.0 + - + +
154A VAL* 3.4 42.8 - - + +
155A PHE 3.8 16.8 - - - +
156A LEU* 4.4 11.0 - - + -
159A TRP 4.1 0.6 + - - +
160A ASP* 1.3 72.2 - - - +
162A GLU* 1.3 71.4 + - - +
163A SER 4.7 0.7 - - - +
187A LEU* 4.0 25.4 - - + -
189A ILE* 3.8 12.6 - - + -
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Residues in contact with GLU 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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122A SER* 5.1 0.2 + - - -
150A LYS* 4.0 8.0 + - - -
160A ASP* 3.5 10.1 - - - +
161A ILE* 1.3 81.7 - - - +
163A SER* 1.3 66.9 + - - +
188A ARG* 2.9 23.7 + - + +
189A ILE 3.6 1.2 - - - -
190A SER* 3.1 43.4 + - - -
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Residues in contact with SER 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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150A LYS* 5.2 1.1 - - - +
161A ILE* 4.0 1.5 - - - +
162A GLU* 1.3 84.4 - - - +
164A PHE* 1.3 62.8 + - - +
165A THR* 4.3 9.1 - - - +
186A GLN 3.6 2.3 - - - +
187A LEU* 3.8 4.4 - - - +
188A ARG* 2.9 46.5 + - - +
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Residues in contact with PHE 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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21A ILE* 3.6 32.5 - - + -
23A LEU* 3.6 50.3 - - + -
127A ILE* 4.6 9.6 - - + -
147A LYS* 3.8 32.2 - - + +
148A VAL 5.5 1.9 - - - -
149A GLY 4.0 6.7 - - - +
150A LYS* 4.8 16.1 - - + +
163A SER* 1.3 73.2 - - - +
165A THR* 1.3 60.9 - - - +
185A TYR* 3.7 33.4 - + + -
186A GLN 3.4 20.9 - - - -
187A LEU* 3.8 15.0 - - + -
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Residues in contact with THR 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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147A LYS* 3.9 15.8 + - - +
163A SER* 4.3 16.8 - - - +
164A PHE* 1.3 76.5 - - - +
166A ALA* 1.3 86.3 + - - +
167A VAL* 5.8 0.3 - - - +
185A TYR* 3.5 8.9 - - - +
186A GLN* 2.9 54.5 + - + +
188A ARG* 5.0 4.0 - - + -
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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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142A ALA* 4.2 15.7 - - + -
144A ASP* 5.6 0.9 - - - +
147A LYS* 3.9 17.1 + - + +
165A THR* 1.3 91.9 + - - +
167A VAL* 1.3 65.0 + - - +
168A VAL* 3.3 11.0 + - + +
183A LEU* 6.4 0.2 - - + -
184A ASP 3.7 5.2 - - - -
185A TYR* 3.6 35.4 - - + +
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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