Contacts of the strand formed by residues 118 - 124 (chain J) in PDB entry 4UJ3
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 VAL 118 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85J VAL 3.2 8.6 + - - +
87J ALA* 2.7 33.3 + - - +
116J ASN 4.1 5.6 - - - +
117J ILE* 1.3 71.4 - - - +
119J ILE* 1.3 61.4 + - - +
149J SER* 5.0 0.2 - - - +
168J ILE* 3.7 19.3 - - + +
171J GLU* 3.7 26.9 - - + +
172J ILE* 3.3 35.2 - - + -
175J ILE* 4.0 28.3 - - + -
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Residues in contact with ILE 119 (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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87J ALA* 3.5 6.1 - - + +
89J LEU* 4.4 9.6 - - + -
106J LEU* 3.6 20.9 - - + -
109J LEU* 3.1 39.9 - - + -
117J ILE* 3.5 19.4 + - + +
118J VAL* 1.3 81.3 - - - +
120J MET* 1.3 69.1 + - - +
147J GLY 4.7 0.9 - - - +
148J LEU* 3.3 33.9 - - + -
149J SER* 3.1 23.3 + - - -
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Residues in contact with MET 120 (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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87J ALA 3.0 7.7 + - - -
88J LEU* 3.4 29.3 - - + -
89J LEU* 3.0 26.9 + - - +
118J VAL 4.2 0.4 + - - -
119J ILE* 1.3 77.6 - - - +
121J LEU* 1.3 69.2 + - - +
122J VAL* 3.6 12.9 + - + +
149J SER* 3.2 29.4 - - - +
150J PHE* 4.2 2.0 - - - +
151J ILE* 3.6 13.0 - - + -
164J ALA* 3.2 50.3 - - + +
167J THR* 4.5 11.0 - - - -
168J ILE* 4.2 12.8 - - + +
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Residues in contact with LEU 121 (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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89J LEU* 3.7 20.0 - - + +
91J TYR* 4.0 25.8 - - + -
99J TYR* 5.0 2.5 - - + -
102J VAL* 4.0 27.4 - - + -
119J ILE 4.2 0.2 - - - -
120J MET* 1.3 71.5 - - - +
122J VAL* 1.3 62.9 + - - +
139J ALA* 4.1 13.2 - - + +
142J PHE* 4.1 23.3 - - + -
143J ALA* 4.3 7.0 - - + -
148J LEU* 4.6 12.4 - - + +
149J SER 2.7 18.4 + - - +
150J PHE* 3.3 23.5 - - + -
151J ILE 3.1 26.9 + - - +
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Residues in contact with VAL 122 (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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27J LEU* 4.4 13.9 - - + -
88J LEU* 4.2 10.8 - - + -
89J LEU 2.9 10.6 + - - +
90J VAL* 3.3 15.4 - - + +
91J TYR* 2.9 33.2 + - - +
120J MET* 3.6 35.9 - - + +
121J LEU* 1.3 79.8 - - - +
123J GLY* 1.3 63.0 + - - +
124J ASN 4.7 0.2 - - - +
151J ILE* 3.4 4.0 - - + +
153J THR* 3.3 39.5 - - + +
164J ALA* 5.2 1.3 - - + -
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Residues in contact with GLY 123 (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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91J TYR* 3.5 32.4 + - - -
93J ILE* 3.6 10.3 - - - +
121J LEU 4.2 0.2 - - - -
122J VAL* 1.3 73.6 - - - +
124J ASN* 1.3 57.9 + - - -
150J PHE* 4.7 0.8 - - - -
151J ILE 3.2 9.6 + - - -
152J GLU* 3.4 5.1 - - - -
153J THR* 2.7 32.9 + - - +
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Residues in contact with ASN 124 (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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22J VAL 2.9 24.6 + - - +
23J GLY* 3.7 8.5 + - - -
27J LEU* 3.7 9.2 - - + +
90J VAL* 4.0 10.3 - - + -
91J TYR 3.0 12.0 + - - +
92J ASP* 3.9 0.2 - - - +
93J ILE* 3.1 21.3 + - - +
122J VAL 3.9 0.2 - - - -
123J GLY* 1.3 73.6 - - - -
125J LYS* 1.3 80.7 + - - +
126J SER 3.4 2.2 - - - -
153J THR* 3.1 21.1 + - - +
155J ALA* 3.1 18.5 + - - +
200J GNP 2.8 36.1 + - - -
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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