Contacts of the strand formed by residues 42 - 48 (chain A) in PDB entry 1LHO
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 SER 42 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39A LYS* 4.8 0.4 - - - +
41A SER* 1.3 71.1 - - - +
43A SER* 1.3 64.4 + - - +
44A PHE* 4.9 1.9 - - - -
56A PHE* 5.0 2.0 - - - -
104A GLU* 3.4 2.7 - - - +
105A VAL* 2.9 35.9 + - - +
141A ILE* 5.7 0.5 - - - +
169A SER 3.2 11.7 - - - -
170A TRP* 3.7 26.0 - - - -
171A LEU* 3.1 21.0 + - - +
301A AOM 2.7 27.7 + - - +
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Residues in contact with SER 43 (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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39A LYS* 5.8 0.5 + - - -
41A SER* 5.6 1.1 + - - -
42A SER* 1.3 76.3 - - - +
44A PHE* 1.3 69.2 + - - +
102A GLN* 5.8 6.1 - - - -
103A VAL 3.1 12.6 - - - -
104A GLU* 4.2 19.0 + - - -
167A ARG 3.6 3.2 + - - +
168A ASP* 3.1 1.2 - - - +
169A SER* 2.9 43.3 + - - +
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Residues in contact with PHE 44 (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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42A SER 5.2 2.2 - - - -
43A SER* 1.3 84.8 - - - +
45A GLU* 1.3 70.5 + - - +
46A VAL* 4.2 9.6 - - + -
55A ILE* 3.5 29.6 - - + -
56A PHE* 4.0 12.8 - + - -
69A LEU* 4.1 6.3 - - + -
102A GLN* 3.6 5.2 - - - +
103A VAL* 2.8 69.8 + - + +
105A VAL* 5.2 1.1 - - + -
165A LEU* 3.4 28.9 - - + -
166A ARG 3.8 0.2 - - - +
167A ARG 3.4 12.3 - - - -
168A ASP* 3.7 11.4 - - + -
170A TRP* 3.5 27.6 - + - -
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Residues in contact with GLU 45 (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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44A PHE* 1.3 79.9 - - - +
46A VAL* 1.3 60.9 + - - +
100A TRP* 3.8 16.2 - - + -
101A HIS 3.0 12.8 - - - +
102A GLN* 4.3 13.3 - - + +
165A LEU* 3.5 7.4 - - - +
166A ARG* 2.5 79.3 + - + +
167A ARG* 3.0 40.1 + - + +
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Residues in contact with VAL 46 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A LEU* 4.1 21.5 - - + -
44A PHE* 4.2 12.6 - - + -
45A GLU* 1.3 76.5 - - - +
47A ARG* 1.3 70.0 + - - +
48A THR* 4.7 10.3 - - + -
55A ILE* 4.8 13.2 - - + -
71A LEU* 6.4 0.9 - - + -
95A LEU* 4.7 13.2 - - + +
99A ARG 3.5 2.8 - - - +
100A TRP* 3.5 3.9 - - - -
101A HIS* 3.0 42.8 + - + +
103A VAL* 4.2 18.8 - - + -
161A LEU* 5.0 3.8 - - + -
164A CYS 3.2 12.6 - - - +
165A LEU* 5.0 0.7 - - + -
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Residues in contact with ARG 47 (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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46A VAL* 1.3 75.5 - - - +
48A THR* 1.3 67.0 + - - +
95A LEU 5.5 0.2 - - - -
98A GLY* 3.3 33.4 + - - +
99A ARG* 3.8 6.5 - - - +
100A TRP* 3.3 59.3 - - + +
163A GLY* 3.2 0.9 - - - -
164A CYS* 2.8 45.3 + - + +
188A CYS* 5.1 9.9 + - - +
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Residues in contact with THR 48 (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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46A VAL* 4.7 8.5 - - + -
47A ARG* 1.3 84.4 - - - +
49A TRP* 1.3 70.8 + - - +
50A ASP* 2.8 26.8 + - - +
71A LEU* 4.1 14.8 - - + -
95A LEU* 3.7 16.4 + - + +
96A ASP* 3.2 13.6 - - - -
98A GLY* 3.0 21.5 + - - -
161A LEU* 4.0 8.3 - - + +
162A ASP 2.7 26.5 + - - -
163A GLY* 3.8 4.7 - - - -
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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