Contacts of the strand formed by residues 122 - 128 (chain W) in PDB entry 4JPB
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 122 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118W PHE* 3.5 24.8 + - - +
119W GLY 3.6 8.3 + - - +
120W LYS* 3.2 15.0 - - - +
121W LYS* 1.3 80.8 - - - +
123W LYS* 1.3 62.8 + - - +
124W GLY* 3.4 13.5 + - - -
134W ILE* 4.1 12.4 - - - +
135W TYR 3.7 4.3 - - - -
136W LEU* 4.6 2.5 - - - -
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Residues in contact with LYS 123 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11W PHE* 5.8 2.7 - - + -
26W ASP* 4.3 7.6 - - - -
109W LEU* 4.1 6.9 - - + +
111W LEU* 3.5 16.6 - - - +
122W SER* 1.3 74.2 - - - +
124W GLY* 1.3 58.0 + - - +
135W TYR* 2.8 64.0 + - + +
136W LEU 4.4 0.9 - - - +
137W ASP* 3.4 47.8 + - + +
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Residues in contact with GLY 124 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109W LEU* 4.8 2.2 - - - -
110W ASP 3.8 8.3 - - - -
111W LEU* 4.0 9.4 - - - -
122W SER* 3.4 9.7 + - - -
123W LYS* 1.3 80.6 - - - +
125W LEU* 1.3 68.9 + - - -
134W ILE* 3.8 5.2 - - - +
135W TYR* 2.9 29.6 + - - +
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Residues in contact with LEU 125 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109W LEU* 3.4 8.8 - - - +
110W ASP* 2.8 56.4 + - + +
111W LEU 5.2 0.2 - - - -
112W THR* 4.0 19.7 - - - +
114W VAL* 4.1 18.8 - - + -
124W GLY* 1.3 79.0 - - - +
126W VAL* 1.3 64.8 + - - +
127W LYS* 5.1 0.2 - - + -
132W LEU* 4.1 38.8 - - + -
133W ILE 3.6 9.6 - - - +
134W ILE* 4.9 16.6 - - + -
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Residues in contact with VAL 126 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13W VAL* 6.1 3.8 - - + -
24W ALA* 6.2 0.7 - - + -
102W LEU* 4.4 18.2 - - + -
104W ILE* 4.3 25.8 - - + -
108W GLN* 3.7 10.3 - - + +
109W LEU* 3.7 18.8 - - + -
125W LEU* 1.3 78.6 - - - +
127W LYS* 1.3 65.6 + - - +
128W THR* 4.8 3.6 - - + -
131W ARG 3.6 5.2 - - - +
132W LEU* 3.7 1.6 - - - -
133W ILE* 2.9 53.5 + - + +
135W TYR* 3.9 15.0 - - + +
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Residues in contact with LYS 127 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108W GLN* 3.4 38.2 + - + +
110W ASP* 3.0 46.4 + - + +
125W LEU* 5.1 0.9 - - + -
126W VAL* 1.3 72.7 - - - +
128W THR* 1.3 60.3 + - - +
129W ASP 4.2 0.4 - - - -
130W GLY* 4.7 10.8 - - - +
131W ARG 4.3 3.1 - - - -
132W LEU* 4.1 21.1 - - + -
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Residues in contact with THR 128 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102W LEU* 4.5 13.2 - - + +
108W GLN* 5.1 5.4 - - - +
126W VAL* 4.5 4.3 - - + +
127W LYS* 1.3 74.9 - - - +
129W ASP* 1.3 81.5 + - - +
130W GLY 3.1 2.0 - - - -
131W ARG* 2.8 38.8 + - + +
133W ILE* 4.1 22.4 - - + -
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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