Contacts of the strand formed by residues 84 - 92 (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 ALA 84 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13J LYS* 3.3 17.7 - - + +
15J VAL* 4.0 24.2 - - + -
81J TYR* 3.0 21.4 + - - +
82J ARG 3.1 2.0 + - - -
83J GLY* 1.3 77.7 - - - +
85J VAL* 1.3 61.1 + - - +
86J GLY 4.2 2.7 - - - +
114J ASP* 4.7 13.2 + - - +
117J ILE* 3.9 27.2 - - + +
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Residues in contact with VAL 85 (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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11J LEU 5.8 0.9 - - - +
12J PHE* 3.6 39.0 - - + -
13J LYS 2.8 14.9 + - - +
83J GLY 3.7 13.0 - - - +
84J ALA* 1.3 73.7 - - - +
86J GLY* 1.3 57.8 + - - +
116J ASN 4.6 1.1 - - - +
117J ILE* 3.8 10.0 - - - +
118J VAL* 3.2 16.8 + - - +
172J ILE* 3.1 31.9 - - + +
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Residues in contact with GLY 86 (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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13J LYS 3.2 4.3 + - - +
14J VAL* 3.1 13.5 - - - -
15J VAL* 3.0 25.3 + - - +
84J ALA* 3.5 1.5 - - - +
85J VAL* 1.3 81.7 - - - +
87J ALA* 1.3 61.3 + - - +
117J ILE* 3.7 5.0 - - - +
118J VAL 3.3 9.6 - - - -
168J ILE* 4.1 1.3 - - - -
172J ILE* 3.4 16.6 - - - -
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Residues in contact with ALA 87 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14J VAL* 4.2 0.2 - - - -
15J VAL* 3.3 17.5 - - + +
17J ILE* 5.1 3.4 - - + -
86J GLY* 1.3 75.2 - - - +
88J LEU* 1.3 61.1 + - - +
89J LEU 3.7 1.0 + - - +
109J LEU* 4.1 24.9 - - + -
117J ILE* 3.7 18.2 - - + -
118J VAL 2.7 12.7 + - - +
119J ILE* 3.5 2.5 - - + +
120J MET 3.0 24.9 + - - -
168J ILE* 3.4 9.0 - - - +
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Residues in contact with LEU 88 (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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14J VAL* 4.1 11.9 - - + -
15J VAL 2.9 8.3 + - - -
16J LEU* 3.3 25.8 - - + -
17J ILE* 3.1 26.6 + - - +
27J LEU* 5.8 3.1 - - + -
87J ALA* 1.3 69.8 - - - +
89J LEU* 1.3 61.5 + - - +
90J VAL* 3.5 9.9 + - + +
120J MET* 3.4 36.8 - - + -
122J VAL* 4.2 5.8 - - + -
164J ALA* 4.9 1.3 - - + +
165J PHE* 3.1 43.7 - - + -
168J ILE* 3.7 24.5 - - + -
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Residues in contact with LEU 89 (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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17J ILE* 3.4 24.9 - - + +
87J ALA 3.7 2.4 + - - +
88J LEU* 1.3 68.9 - - - +
90J VAL* 1.3 68.6 + - - +
102J VAL* 3.9 39.5 - - + +
105J TRP* 4.1 22.2 - - + -
106J LEU* 3.7 36.3 - - + +
109J LEU* 4.8 0.9 - - + -
119J ILE* 4.4 13.0 - - + -
120J MET 3.0 15.0 + - - +
121J LEU* 3.7 10.5 - - + +
122J VAL 2.9 26.2 + - - +
148J LEU* 5.4 0.9 - - + -
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Residues in contact with VAL 90 (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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16J LEU* 4.6 1.8 - - + -
17J ILE 2.9 11.7 + - - +
18J GLY* 3.4 19.4 - - - -
19J ASP 3.9 1.4 + - - -
22J VAL* 3.4 39.6 - - + +
24J LYS* 4.2 8.7 - - + -
27J LEU* 3.6 26.9 - - + -
88J LEU* 3.7 17.3 - - + +
89J LEU* 1.3 81.6 - - - +
91J TYR* 1.3 74.4 + - - +
98J THR 4.8 1.6 - - - +
102J VAL* 5.3 0.2 - - - +
105J TRP* 5.3 0.3 - - - -
122J VAL* 3.3 16.6 - - + +
124J ASN* 4.0 10.8 - - + -
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Residues in contact with TYR 91 (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* 3.8 10.1 - - - -
90J VAL* 1.3 79.1 - - - +
92J ASP* 1.3 70.2 + - - +
93J ILE* 3.8 17.7 - - + +
98J THR* 3.4 25.4 - - - +
99J TYR* 3.7 37.0 - + + -
102J VAL* 4.0 5.2 - - + -
121J LEU* 4.0 33.7 - - + -
122J VAL 2.9 22.2 + - - -
123J GLY* 3.5 19.1 - - - -
124J ASN* 3.0 24.9 + - - +
134J VAL* 3.8 10.5 - - + +
139J ALA* 3.5 17.8 - - - +
150J PHE* 3.7 9.4 - + - -
152J GLU* 3.9 10.0 + - - -
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Residues in contact with ASP 92 (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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21J GLY 4.1 1.3 - - - +
22J VAL* 3.6 15.9 - - + +
91J TYR* 1.3 73.9 - - - +
93J ILE* 1.3 58.3 + - - +
94J ALA* 3.0 17.7 + - - +
95J LYS* 2.8 56.4 + - + +
98J THR* 2.7 22.9 + - + +
124J ASN 4.2 2.0 - - - -
125J LYS* 2.8 48.2 + - - +
134J VAL* 4.9 0.5 - - - +
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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