Contacts of the strand formed by residues 148 - 153 (chain J) in PDB entry 6LTJ
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 ALA 148 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118J HIS 3.4 4.4 + - - +
119J PRO* 3.2 15.2 - - + +
120J VAL* 3.0 19.5 + - - +
146J ILE* 4.1 4.0 - - - +
147J PRO* 1.3 84.7 - - + +
149J PHE* 1.3 66.3 + - - +
410J TRP* 3.5 18.2 - - + +
411J ILE 3.3 20.0 - - - +
412J SER* 4.3 6.3 - - - -
413J LYS 5.0 0.2 - - - +
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Residues in contact with PHE 149 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120J VAL* 2.9 30.5 - - + +
122J MET* 5.7 7.9 - - + -
136J LEU* 5.3 1.6 - - + -
137J THR* 3.5 41.1 - - + -
140J MET* 3.6 34.3 - - + -
141J PHE* 3.5 39.5 - + - -
146J ILE 5.4 1.6 - - - +
148J ALA* 1.3 77.0 - - - +
150J PHE* 1.3 82.3 + - - +
151J LEU* 4.8 14.8 - - + -
410J TRP* 3.9 4.9 + - - +
411J ILE* 3.3 33.4 + - + +
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Residues in contact with PHE 150 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120J VAL 2.9 4.4 + - - -
121J LEU* 3.2 22.2 - - + +
122J MET 2.9 24.5 + - - +
149J PHE* 1.3 84.8 - - - +
151J LEU* 1.3 85.0 + - + +
152J CYS* 4.3 11.9 - - + -
400J LEU* 6.5 1.1 - - + -
409J MET* 5.0 10.1 - - + -
410J TRP* 4.0 33.9 - + + -
411J ILE* 4.0 24.9 - - + -
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Residues in contact with LEU 151 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121J LEU* 5.0 0.2 - - - -
122J MET* 2.7 18.4 - - + +
124J GLU* 3.3 34.1 - - - +
133J ARG* 3.4 40.6 - - + +
136J LEU* 4.7 15.9 - - + -
137J THR* 4.9 5.6 - - + -
149J PHE* 4.5 17.7 - - + -
150J PHE* 1.3 104.3 - - + +
152J CYS* 1.3 66.4 + - - +
153J LYS* 6.2 1.6 - - + +
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Residues in contact with CYS 152 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121J LEU* 5.3 4.9 - - - -
122J MET 2.9 7.3 + - - -
123J SER* 2.7 20.1 + - - -
124J GLU* 2.9 21.6 + - - +
150J PHE* 4.3 13.0 - - + -
151J LEU* 1.3 82.4 - - - +
153J LYS* 1.3 75.7 + - - +
156J VAL* 3.7 14.1 - - + -
157J LEU* 3.6 29.4 - - - -
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Residues in contact with LYS 153 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123J SER* 3.0 4.3 - - - -
124J GLU* 3.3 13.0 - - - +
125J ALA 5.4 0.4 - - - +
126J PRO* 3.7 42.0 - - + -
128J ASN* 6.2 0.7 - - - -
133J ARG* 4.9 20.0 - - - +
151J LEU* 6.2 1.2 - - + +
152J CYS* 1.3 81.7 - - - +
154J THR* 1.3 66.1 + - - +
155J ALA 3.1 2.2 - - - +
156J VAL* 3.1 27.4 + - + +
157J LEU 3.6 0.3 + - - -
186J TYR* 5.8 5.1 + - - -
187J VAL* 4.2 31.2 - - + -
189J GLN* 6.0 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