Contacts of the strand formed by residues 92 - 102 (chain J) in PDB entry 1P84
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 92 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39J ARG* 4.3 1.6 - - + -
40J LEU 3.0 31.9 - - - +
41J PHE* 3.7 16.8 - - + +
42J PRO* 4.7 2.7 - - - -
90J ASP 3.5 3.4 + - - -
91J THR* 1.3 78.3 - - - +
93J THR* 1.3 63.7 + - - +
94J TYR* 3.1 25.5 - - + -
117J THR* 5.1 1.3 - - - -
118J VAL 3.2 24.1 + - - +
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Residues in contact with THR 93 (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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39J ARG* 3.5 0.7 - - - -
40J LEU* 2.7 59.2 + - + +
92J ALA* 1.3 73.8 - - - +
94J TYR* 1.3 60.5 + - - +
95J TYR* 3.7 15.9 + - - -
115J GLY 5.4 1.1 - - - -
116J THR 3.5 7.6 - - - -
117J THR* 3.2 37.9 - - + +
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Residues in contact with TYR 94 (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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6J GLU* 3.2 6.1 - - - +
18J LEU* 3.8 13.4 - - + +
20J LEU* 3.5 24.7 - - + -
37J TRP* 4.7 3.6 - + + -
38J ILE 3.7 5.2 - - - -
39J ARG* 3.1 52.0 + - + -
49J VAL* 5.2 4.7 - - + -
81J LEU* 3.5 30.1 - - + -
83J LEU* 3.5 13.2 - - + +
90J ASP* 3.2 15.1 + - - +
92J ALA* 3.1 24.7 - - + -
93J THR* 1.3 76.5 - - - +
95J TYR* 1.3 61.1 + - - +
115J GLY* 3.3 3.5 - - - -
116J THR 2.8 39.8 + - - +
118J VAL* 3.6 17.9 - - + -
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Residues in contact with TYR 95 (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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6J GLU* 3.6 2.9 - - - -
37J TRP* 3.0 11.5 - - - -
38J ILE* 2.7 63.1 + - + +
40J LEU* 4.0 24.0 - - + +
46J LEU* 5.0 2.9 - - + -
93J THR* 3.7 27.5 + - - -
94J TYR* 1.3 76.0 - - - +
96J CYS* 1.3 59.7 + - - +
112J TRP* 4.0 11.0 - + + -
113J GLY 3.6 13.7 - - - -
114J GLN 3.7 3.8 - - - -
115J GLY* 3.5 25.1 - - - -
38K GLN* 4.7 4.8 - - + +
42K GLY* 2.6 37.5 + - - -
44K ILE* 3.6 22.8 - - + +
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Residues in contact with CYS 96 (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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4J LEU* 3.5 10.7 - - - +
6J GLU* 3.4 25.3 + - - -
22J CYS* 2.0 50.0 - - + -
36J ASN 3.2 9.2 - - - +
37J TRP* 3.4 19.1 - - + -
79J PHE* 3.9 4.0 - - + -
95J TYR* 1.3 73.2 - - - +
97J ALA* 1.3 59.9 + - - +
112J TRP* 4.5 0.9 - - - -
113J GLY 2.7 29.1 + - - -
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Residues in contact with ALA 97 (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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4J LEU* 3.7 5.3 - - - +
35J TRP* 3.7 3.3 - - - -
36J ASN* 2.6 45.2 + - + +
38J ILE* 6.0 0.4 - - + -
79J PHE* 4.7 0.8 - - - -
95J TYR 4.3 0.2 - - - -
96J CYS* 1.3 76.0 - - - +
98J ARG* 1.3 58.0 + - - +
109J MET* 4.3 14.8 - - + -
111J TYR 3.0 15.0 - - - +
112J TRP* 3.6 35.9 - - + -
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Residues in contact with ARG 98 (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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130E ASN* 3.1 36.5 + - - +
131E SER* 4.8 0.6 - - - +
2J VAL* 5.0 2.8 - - - +
4J LEU* 4.2 1.4 - - + +
27J TYR* 3.6 19.6 - - - -
33J TYR* 3.5 25.7 - - + -
34J TYR 3.2 12.8 - - - +
35J TRP* 3.4 43.5 - - + -
97J ALA* 1.3 72.4 - - - +
99J SER* 1.3 67.1 + - - +
100J GLU* 3.9 8.2 + - - +
109J MET* 3.1 5.1 - - - -
110J ASP* 2.7 61.8 + - - +
111J TYR* 2.9 36.4 + - + +
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Residues in contact with SER 99 (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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33J TYR* 3.2 4.0 - - - +
34J TYR* 2.8 46.4 + - - +
36J ASN* 3.2 23.1 + - - +
98J ARG* 1.3 73.6 - - - +
100J GLU* 1.3 61.7 + - - +
107J TYR* 4.2 3.8 - - - -
108J ALA 2.9 18.4 - - - -
109J MET* 3.5 12.1 - - - -
96K TRP* 3.6 16.4 - - - -
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Residues in contact with GLU 100 (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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126E ILE* 5.4 0.7 - - - +
130E ASN* 2.8 35.2 + - - +
33J TYR* 3.7 18.2 - - + -
98J ARG* 4.0 10.3 - - - +
99J SER* 1.3 74.8 - - - +
101J TYR* 1.3 62.6 + - - +
102J TYR* 4.2 20.4 - - + -
106J GLY 3.8 1.2 - - - +
107J TYR* 3.2 25.3 - - - +
108J ALA* 2.8 24.9 + - - +
110J ASP* 3.3 36.2 - - - +
46K LEU* 5.5 1.2 - - - +
49K TYR* 5.3 7.4 - - - -
55K HIS* 5.5 3.6 + - - -
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Residues in contact with TYR 101 (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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144E ALA* 3.5 23.7 - - - +
33J TYR* 3.7 9.2 - - + -
34J TYR* 4.0 26.2 - + + -
100J GLU* 1.3 76.9 - - - +
102J TYR* 1.3 71.8 + - - +
103J SER* 3.6 32.9 + - - -
106J GLY* 3.8 21.5 - - - -
107J TYR* 3.8 31.9 - + + -
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Residues in contact with TYR 102 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126E ILE* 3.9 5.3 - - + +
130E ASN* 3.0 32.1 + - + +
143E ASP* 2.8 20.5 + - - +
144E ALA* 3.7 23.6 - - + -
147E VAL* 3.6 36.3 - - + -
148E LYS 3.9 4.9 - - - +
150E PRO* 3.4 39.7 - - + -
33J TYR* 5.0 2.2 - + - -
100J GLU* 4.2 21.5 - - + -
101J TYR* 1.3 79.2 - - - +
103J SER* 1.3 57.5 + - - +
104J VAL 2.9 3.8 + - - -
105J THR* 3.5 17.5 - - - +
106J GLY* 2.8 36.8 + - - -
49K TYR* 5.5 3.1 - + - -
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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