Contacts of the strand formed by residues 121 - 127 (chain B) 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 SER 121 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117B ASN* 3.1 38.4 + - - +
118B PHE 4.5 2.5 - - - -
119B GLY 3.1 14.2 + - - -
120B SER* 1.3 75.3 - - - +
122B TRP* 1.3 62.5 + - - +
138B THR 3.1 17.3 - - - -
139B SER* 4.3 1.8 - - - -
140B ASN 4.1 4.3 - - - +
158B LEU* 2.8 38.1 + - - +
159B TRP* 3.4 13.6 + - - +
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Residues in contact with TRP 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B GLN* 3.1 22.2 + - - -
72B ASN* 3.5 40.6 - - + +
73B HIS* 3.6 23.3 - + - -
76B TYR* 3.8 10.8 - - + -
117B ASN* 3.0 9.5 + - - -
121B SER* 1.3 78.5 - - - +
123B THR* 1.3 59.4 + - - +
124B TRP* 3.3 24.6 - + + +
137B ASN* 3.5 0.2 - - - -
138B THR* 2.8 41.0 + - - +
140B ASN 2.9 29.4 + - - -
142B ALA 4.1 5.6 - - - -
155B THR* 3.5 17.0 - - + +
156B VAL 3.5 5.8 - - - -
157B ASP* 3.4 47.3 - - + -
158B LEU* 4.4 0.4 - - - +
159B TRP* 3.5 4.0 - - - +
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Residues in contact with THR 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B LEU* 3.8 32.9 - - + +
114B ALA* 3.4 9.5 - - + +
117B ASN* 3.1 9.4 + - - -
122B TRP* 1.3 70.6 - - - +
124B TRP* 1.3 61.7 + - - +
135B ILE* 3.6 20.4 - - + -
136B VAL 3.7 2.9 - - - -
137B ASN* 2.7 24.7 + - - +
155B THR* 3.4 2.1 + - - -
156B VAL* 2.9 38.8 + - - +
158B LEU* 3.2 17.0 - - - +
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Residues in contact with TRP 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B TRP* 3.8 11.9 - + - -
72B ASN* 3.3 36.3 - - + -
75B PHE* 3.6 21.8 - + - -
110B LEU* 5.2 2.7 - - - -
122B TRP* 3.3 24.3 - + + +
123B THR* 1.3 74.8 - - - +
125B LEU* 1.3 60.2 + - - +
126B VAL* 3.8 8.1 - - + -
135B ILE* 3.2 10.6 - - - +
136B VAL* 2.8 56.1 + - + +
138B THR* 2.9 27.2 + - + -
142B ALA 4.1 0.4 - - - -
143B THR* 3.6 11.0 - - - -
144B PRO* 3.2 32.4 - - + +
152B PRO* 4.4 3.8 - - + -
154B LEU 3.4 10.1 - - - +
155B THR* 3.3 35.2 - - + -
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Residues in contact with LEU 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B VAL* 4.5 10.5 - - + -
96B ILE* 5.0 0.7 - - + -
100B TRP* 3.9 11.2 - - + -
106B PHE* 3.7 37.9 - - + -
110B LEU* 5.0 5.7 - - + +
124B TRP* 1.3 73.8 - - - +
126B VAL* 1.4 62.6 + - - +
133B LEU* 4.1 25.6 - - + -
134B ASP 3.5 15.5 - - - +
135B ILE* 4.6 1.3 - - + +
152B PRO* 4.0 0.5 - - - +
153B ILE* 2.8 48.4 + - + -
154B LEU* 2.9 38.3 + - + +
184B TRP* 4.9 1.6 - - + -
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Residues in contact with VAL 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B TRP* 3.8 8.1 - - + -
125B LEU* 1.4 79.8 - - - +
127B LYS* 1.3 60.5 - - - +
128B LEU* 3.7 20.6 - - + -
133B LEU* 3.3 6.8 - - - +
134B ASP* 2.8 45.4 + - + +
136B VAL* 3.7 35.0 - - + -
144B PRO* 3.9 15.9 - - + -
150B VAL* 3.5 22.7 - - + -
151B THR 3.3 7.4 - - - +
152B PRO* 4.3 2.2 - - + -
153B ILE* 3.8 5.8 - - - -
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Residues in contact with LYS 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B VAL* 1.3 72.6 - - - +
128B LEU* 1.3 78.3 + - - +
129B ALA* 5.5 1.6 + - - +
131B GLY* 3.9 16.2 - - - +
132B SER 3.4 3.6 - - - +
133B LEU* 4.2 1.8 - - - -
149B GLY 4.0 0.2 - - - +
150B VAL* 3.6 1.9 - - - -
151B THR* 2.7 65.0 + - - +
153B ILE* 3.7 15.0 - - + +
190B ASN 4.6 0.9 - - - -
191B PHE* 3.5 58.1 - - + +
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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