Contacts of the strand formed by residues 151 - 157 (chain A) in PDB entry 3LIO
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 151 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126A VAL* 3.3 2.7 - - - -
127A LYS* 2.8 62.1 + - - -
149A GLY 4.7 3.8 + - - -
150A VAL* 1.4 74.4 + - - +
152A PRO* 1.3 76.6 - - + +
153A ILE* 3.5 4.8 + - + +
190A ASN* 3.5 25.8 - - + +
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Residues in contact with PRO 152 (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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71A TRP* 3.9 17.0 - - + -
75A PHE* 3.4 31.1 - - + -
124A TRP* 4.4 4.0 - - + -
125A LEU 4.0 4.3 - - - +
126A VAL* 4.2 6.5 - - + -
144A PRO* 3.8 25.8 - - + -
145A LEU* 3.9 23.3 - - + +
150A VAL 3.6 8.7 - - - +
151A THR* 1.3 89.7 - - + +
153A ILE* 1.4 59.7 + - - +
190A ASN* 3.5 15.2 - - - +
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Residues in contact with ILE 153 (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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75A PHE* 3.6 4.7 - - - -
92A VAL* 4.5 6.1 - - + -
125A LEU* 2.8 35.4 + - + +
126A VAL 3.9 3.4 - - - -
127A LYS* 3.8 21.8 - - + +
133A LEU* 4.2 8.5 - - + -
151A THR* 3.6 15.7 - - + +
152A PRO* 1.4 80.2 - - - +
154A LEU* 1.3 67.1 + - - +
186A PHE* 4.1 0.7 - - - -
187A ALA* 3.6 32.7 - - + +
190A ASN* 3.1 24.8 + - - +
191A PHE* 3.6 34.8 - - + +
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Residues in contact with LEU 154 (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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75A PHE* 3.6 9.2 - - - -
79A SER* 3.6 30.5 - - - +
106A PHE* 5.8 1.8 - - + -
124A TRP* 3.4 7.1 - - - -
125A LEU* 3.0 43.1 + - + +
153A ILE* 1.3 86.2 - - + +
155A THR* 1.3 63.8 + - - +
178A PHE* 5.0 8.1 - - + -
179A TRP* 6.3 0.4 - - + -
182A VAL* 3.5 24.7 - - + -
183A ASN 3.6 22.2 - - - +
184A TRP* 3.9 20.4 - - + -
186A PHE* 4.2 4.0 - - + -
187A ALA* 3.8 11.4 - - + -
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Residues in contact with THR 155 (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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72A ASN 4.2 1.6 - - - +
75A PHE* 3.8 11.9 - - + -
76A TYR* 3.6 39.2 - - + +
79A SER* 3.2 19.1 + - - -
122A TRP* 3.5 24.8 - - + +
123A THR 3.3 11.2 + - - -
124A TRP* 3.4 29.2 - - + -
154A LEU* 1.3 77.7 - - - +
156A VAL* 1.3 68.8 + - - +
178A PHE* 3.8 4.1 - - - -
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Residues in contact with VAL 156 (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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76A TYR* 4.2 4.7 - - - -
110A LEU* 4.6 10.5 - - + -
114A ALA* 4.5 6.3 - - + -
122A TRP* 3.5 5.5 - - - -
123A THR* 2.9 51.0 + - + +
155A THR* 1.3 72.6 + - - +
157A ASP* 1.3 63.6 + - - +
158A LEU* 3.5 17.9 + - + +
174A TYR* 5.0 4.0 - - + +
175A LEU* 4.7 6.3 - - + -
178A PHE* 3.2 52.7 - - + -
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Residues in contact with ASP 157 (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 HIS* 2.8 14.5 + - - -
73A HIS* 3.4 1.9 + - - -
76A TYR* 3.5 26.4 - - + -
122A TRP* 3.4 28.5 - - + -
156A VAL* 1.3 70.5 - - - +
158A LEU* 1.3 59.5 + - - +
159A TRP* 3.1 32.0 + - - +
162A ALA* 3.5 10.3 - - + +
174A TYR* 2.7 32.1 + - - -
5000A FE 2.0 31.7 - - - -
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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