Contacts of the strand formed by residues 26 - 31 (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 THR 26 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A GLU 4.1 5.2 + - - -
25A CYS* 1.4 76.0 + - - +
27A LEU* 1.3 66.8 + - - +
28A ILE* 3.4 22.6 + - + -
50A LYS 2.8 7.5 + - - -
51A TYR* 3.4 29.7 + - + +
52A GLY 2.9 24.9 + - - +
103A TYR* 3.4 4.6 - - - -
105A LYS* 3.5 29.2 - - + +
106A ILE 4.2 0.9 - - - +
107A MET* 4.0 7.9 - - + +
201A MET* 5.5 1.6 - - - -
206A ILE* 5.1 7.2 - - + +
265A TYR* 5.8 1.1 - - - +
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Residues in contact with LEU 27 (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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11A LEU* 3.7 29.4 - - + -
26A THR* 1.3 73.4 - - - +
28A ILE* 1.3 62.6 + - - +
29A LEU* 3.6 26.1 + - + -
52A GLY 3.9 8.1 - - - -
53A VAL* 4.1 4.3 - - - +
54A PHE* 4.5 1.6 - - + +
80A ILE* 5.2 6.5 - - - +
83A ILE* 3.6 26.5 - - + -
84A VAL 5.1 2.7 - - - +
103A TYR* 3.4 29.3 - - + -
105A LYS 2.9 7.1 + - - -
106A ILE* 3.4 25.7 - - + +
107A MET 2.8 25.3 + - - +
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Residues in contact with ILE 28 (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* 3.4 20.2 - - + +
27A LEU* 1.3 72.0 - - - +
29A LEU* 1.3 63.8 + - - +
30A THR* 3.8 2.8 + - - +
39A ALA* 4.3 11.7 - - + -
43A LEU* 4.4 1.3 - - + -
51A TYR* 4.1 13.5 - - + -
52A GLY 2.9 20.2 + - - +
53A VAL* 3.4 11.1 - - + -
54A PHE 3.1 23.7 + - - +
107A MET* 2.9 68.6 - - + -
109A MET* 4.0 13.5 - - + -
198A PHE* 4.2 10.1 - - + -
201A MET* 4.7 0.4 - - - -
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Residues in contact with LEU 29 (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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27A LEU* 3.6 25.8 + - + -
28A ILE* 1.3 74.0 - - - +
30A THR* 1.3 59.0 + - - +
54A PHE* 3.5 28.9 - - + +
56A LEU* 4.5 9.9 - - + -
80A ILE* 4.0 26.5 - - + -
83A ILE* 5.6 0.9 - - + -
106A ILE* 4.3 13.9 - - + -
107A MET 2.6 16.0 + - - +
108A ILE* 3.4 9.7 - - + +
109A MET* 2.8 28.2 + - - +
119A ILE* 4.5 6.3 - - + -
123A LEU* 3.1 32.5 - - + -
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Residues in contact with THR 30 (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 7.3 + - - +
29A LEU* 1.3 76.4 - - - +
31A GLU* 1.4 57.4 + - - +
32A GLY 3.6 6.5 - - - +
35A ALA* 2.9 19.5 - - + +
36A LYS* 2.9 40.7 - - + +
39A ALA* 3.8 18.7 - - - +
53A VAL* 5.3 2.8 - - - +
54A PHE 3.1 13.6 + - - -
55A PRO* 4.2 9.3 - - + +
56A LEU* 2.7 36.3 + - - +
109A MET* 3.7 4.0 - - + +
119A ILE* 4.9 2.2 - - - -
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Residues in contact with GLU 31 (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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30A THR* 1.4 75.7 - - - +
32A GLY* 1.3 63.0 + - - +
35A ALA* 2.9 17.5 + - - +
56A LEU* 3.2 8.3 - - + +
57A ARG 5.3 0.9 - - - +
58A GLY 4.6 10.5 - - - +
59A LYS* 4.3 18.2 + - + +
109A MET 2.9 17.9 + - - +
110A THR* 3.3 24.3 - - - +
111A ASP 4.2 8.1 + - - +
115A ASP 4.5 0.7 - - - +
116A GLY 4.2 4.3 - - - +
117A SER* 4.0 7.0 - - - -
118A HIS* 3.6 14.9 + - - +
119A ILE* 3.2 44.6 + - + +
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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