Contacts of the strand formed by residues 105 - 110 (chain A) in PDB entry 1LWZ
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 LYS 105 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A THR 3.7 6.3 - - - +
24A GLU* 4.9 5.4 - - - +
25A CYS 3.0 6.4 + - - +
26A THR* 3.5 15.8 - - + +
27A LEU 2.9 22.0 + - - -
96A ASP* 3.2 39.0 + - - -
103A TYR* 3.4 3.0 - - - +
104A GLY* 1.3 92.6 - - - +
106A ILE* 1.3 70.9 + - - +
138A ARG* 3.4 9.1 + - - +
139A PHE* 2.8 27.6 - - - +
205A ARG 4.2 4.8 + - - -
206A ILE* 2.9 48.6 - - + +
207A GLN 3.3 12.7 - - - +
208A PHE 5.1 3.6 + - - -
209A LYS* 5.4 5.4 - - - +
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Residues in contact with ILE 106 (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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26A THR* 4.2 2.5 - - - +
27A LEU* 3.4 34.1 - - + +
29A LEU* 4.3 17.9 - - + -
80A ILE* 5.1 10.5 - - + -
84A VAL* 4.8 16.8 - - + -
103A TYR* 4.9 0.9 - - + -
105A LYS* 1.3 85.5 - - - +
107A MET* 1.3 69.4 + - - +
123A LEU* 5.1 5.2 - - + -
127A ILE* 5.8 2.9 - - + -
139A PHE* 2.9 44.7 + - + +
140A LEU* 4.9 1.6 - - + -
141A GLU* 2.7 40.5 + - + +
206A ILE* 4.6 0.3 - - - +
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Residues in contact with MET 107 (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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26A THR* 4.0 4.0 - - + -
27A LEU 2.8 4.5 + - - +
28A ILE* 2.9 43.1 - - + -
29A LEU* 2.6 32.1 + - - -
106A ILE* 1.3 75.4 - - - +
108A ILE* 1.3 58.9 + - - +
109A MET* 3.0 43.5 - - + -
141A GLU* 2.9 13.2 - - + -
197A TYR* 3.2 47.1 - - + +
198A PHE* 3.4 9.2 - - + -
201A MET* 3.5 11.7 - - - -
265A TYR* 3.8 2.7 - - - +
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Residues in contact with ILE 108 (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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29A LEU* 3.4 5.6 - - + +
106A ILE* 5.2 0.4 - - + -
107A MET* 1.3 74.7 - - - +
109A MET* 1.3 67.8 + - - +
110A THR* 4.2 7.7 + - + +
119A ILE* 3.6 30.1 - - + -
120A LYS* 3.8 24.7 - - + -
123A LEU* 3.2 37.7 - - + -
141A GLU* 2.6 40.3 + - - +
142A GLU* 3.0 22.7 - - - +
143A PHE* 3.5 16.6 + - - +
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Residues in contact with MET 109 (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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28A ILE* 4.0 6.3 - - + -
29A LEU 2.8 12.9 + - - +
30A THR* 3.7 2.6 - - - -
31A GLU* 2.9 31.2 + - - +
35A ALA* 3.6 16.0 - - + +
38A LEU* 3.8 29.2 - - + +
39A ALA* 3.5 33.4 - - + -
107A MET* 3.0 35.4 - - + -
108A ILE* 1.3 75.6 - - - +
110A THR* 1.3 62.3 + - - +
111A ASP* 5.9 2.7 - - + +
143A PHE* 3.9 35.9 - - + -
194A ALA* 5.2 1.8 - - + -
198A PHE* 4.5 1.6 - - + -
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Residues in contact with THR 110 (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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31A GLU* 3.3 13.9 - - - +
108A ILE* 4.1 15.8 + - + +
109A MET* 1.3 78.6 - - - +
111A ASP* 1.4 69.9 + - - +
115A ASP* 3.2 18.6 + - - -
117A SER* 2.8 30.3 + - - +
119A ILE* 3.3 28.0 - - + -
120A LYS* 4.8 0.4 - - + -
142A GLU* 4.9 5.0 + - - +
143A PHE* 5.6 5.9 + - - +
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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