Contacts of the strand formed by residues 109 - 116 (chain A) in PDB entry 1LVB
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 ILE 109 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107A GLU* 3.9 19.7 - - + -
108A ARG* 1.3 79.6 - - - +
110A CYS* 1.3 63.4 + - - +
128A THR* 3.4 6.3 - - - +
129A SER* 2.8 44.6 + - - +
130A CYS 4.1 2.5 - - - +
131A THR* 3.8 30.3 - - + -
142A HIS* 3.8 15.7 - - + -
144A ILE* 3.9 9.2 - - + +
155A LEU* 3.7 27.1 - - + -
156A VAL 3.3 12.1 - - - +
157A SER* 4.7 0.9 - - - -
158A THR* 4.5 1.3 - - - +
164A VAL* 4.3 19.5 - - + -
179A PHE* 3.9 6.1 - - + -
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Residues in contact with CYS 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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11A TYR* 3.6 29.6 - - - -
109A ILE* 1.3 76.0 - - - +
111A LEU* 1.3 59.1 + - - +
112A VAL* 4.5 1.3 - - - -
125A VAL* 3.4 23.6 - - + -
126A SER* 3.5 26.2 - - - +
127A ASP 3.9 4.3 - - - +
128A THR* 4.7 1.3 - - - +
144A ILE* 3.6 7.0 - - - -
155A LEU* 3.4 3.7 - - - -
156A VAL* 2.8 42.5 + - - -
158A THR* 4.6 7.6 - - - +
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Residues in contact with LEU 111 (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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110A CYS* 1.3 73.1 - - - +
112A VAL* 1.3 61.3 + - - +
113A THR* 3.9 19.0 + - - +
124A MSE 3.8 1.4 - - - +
125A VAL* 3.4 2.5 - - - -
126A SER* 2.8 33.2 + - - +
142A HIS* 5.6 0.4 - - - +
144A ILE* 3.5 23.0 - - + +
145A GLN 3.9 11.9 - - - +
146A THR* 3.8 25.8 - - + -
150A GLN* 4.9 8.5 - - + +
153A SER* 3.8 25.4 - - - +
154A PRO 3.4 16.2 - - - +
155A LEU* 4.0 16.2 - - + -
167A HIS* 4.5 7.2 - - + -
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Residues in contact with VAL 112 (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 TYR* 3.7 27.1 - - + +
14A ILE* 4.0 13.5 - - + -
15A SER* 3.5 40.4 - - - +
18A ILE* 3.5 1.7 - - + +
110A CYS* 4.5 0.7 - - - -
111A LEU* 1.3 74.6 - - - +
113A THR* 1.3 65.7 + - - +
124A MSE 3.5 7.0 - - - +
125A VAL* 4.1 7.4 - - + -
153A SER* 3.7 2.9 - - - -
154A PRO* 3.0 38.9 + - + +
156A VAL* 3.6 24.9 - - + -
401A GOL 4.2 4.0 - - - +
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Residues in contact with THR 113 (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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15A SER* 4.2 2.3 - - - -
18A ILE* 3.9 3.8 - - - -
33A TYR* 5.8 1.6 - - + -
111A LEU* 3.9 13.6 + - - +
112A VAL* 1.3 74.4 + - - +
114A THR* 1.3 80.4 + - - +
115A ASN* 5.2 4.7 - - + -
123A SER* 3.2 6.1 - - - -
124A MSE 3.0 48.9 + - + +
150A GLN* 3.5 29.5 + - + +
153A SER* 3.7 17.7 + - - +
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Residues in contact with THR 114 (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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15A SER* 2.9 25.7 + - - +
18A ILE* 3.5 23.4 - - + +
33A TYR* 3.2 27.4 + - - -
60A LEU* 5.7 2.5 - - + -
113A THR* 1.3 82.3 + - - +
115A ASN* 1.3 65.4 + - - +
116A PHE* 3.8 30.3 - - + -
121A MSE 4.3 9.0 - - + -
122A SER 3.3 7.9 - - - +
123A SER* 3.1 18.6 + - - +
153A SER* 5.5 0.4 + - - -
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Residues in contact with ASN 115 (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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33A TYR* 4.0 12.6 + - - +
113A THR* 5.2 4.9 - - + -
114A THR* 1.3 76.7 - - - +
116A PHE* 1.3 64.9 + - - +
117A GLN* 2.9 39.1 + - - +
121A MSE 3.3 6.1 - - - +
122A SER* 2.7 49.8 + - - +
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Residues in contact with PHE 116 (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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18A ILE 3.9 10.5 - - - -
19A CYS 4.7 0.9 - - - -
20A HIS* 4.0 21.1 - - + -
33A TYR* 4.8 6.2 + + - -
58A GLN* 3.4 44.7 - - + +
59A SER* 3.7 36.6 - - - -
60A LEU* 4.1 15.5 - - + -
114A THR* 3.8 23.8 - - + -
115A ASN* 1.3 77.7 + - - +
117A GLN* 1.3 71.5 + - - +
120A SER 4.2 2.0 - - - -
121A MSE 4.1 11.4 - - + +
12B ASN* 3.7 22.9 - - - +
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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