Contacts of the strand formed by residues 129 - 136 (chain D) in PDB entry 4JDA
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 ILE 129 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36D ILE* 4.8 6.5 - - + -
40D HIS* 3.9 38.1 - - + +
66D TRP* 3.4 6.5 - - - -
122D VAL* 3.7 19.7 - - + +
124D ASP* 2.9 35.7 + - + -
127D LYS* 3.7 27.1 - - + +
128D ARG* 1.3 76.6 - - - +
130D LEU* 1.3 67.4 + - - +
147D VAL* 4.2 14.1 - - + -
148D THR 3.3 9.2 - - - +
149D SER* 3.3 26.7 - - - -
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Residues in contact with LEU 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66D TRP* 3.8 5.2 - - + -
69D VAL* 3.2 43.1 - - + +
70D ARG* 3.8 17.3 - - - +
72D PHE* 4.6 14.4 - - + -
103D ARG* 5.9 0.7 - - - +
120D LEU* 4.0 12.3 - - + -
122D VAL 3.2 9.2 - - - +
123D LEU* 4.0 13.5 - - + -
129D ILE* 1.3 75.6 - - - +
131D SER* 1.3 84.7 + - - +
132D PHE* 4.3 17.5 - - + -
147D VAL* 3.4 1.4 - - - -
148D THR* 2.9 35.7 + - - +
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Residues in contact with SER 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120D LEU* 3.6 2.4 - - - +
121D GLU* 2.7 38.3 + - - +
122D VAL* 2.9 36.6 + - - +
130D LEU* 1.3 81.8 - - - +
132D PHE* 1.3 54.0 + - - +
145D ARG* 5.0 7.3 - - - -
146D SER 2.8 20.4 + - - -
147D VAL* 3.4 17.4 - - - +
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Residues in contact with PHE 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72D PHE* 4.0 17.3 - + + -
79D LYS* 3.8 11.2 - - - -
103D ARG* 3.8 22.9 - - - -
118D GLU* 3.5 26.5 - - + -
119D ILE 3.2 14.1 - - - +
120D LEU* 4.3 0.2 - - - -
121D GLU* 4.2 2.2 - - - +
130D LEU* 4.3 13.9 - - + -
131D SER* 1.3 74.6 - - - +
133D ARG* 1.3 63.6 + - - +
134D VAL* 4.2 17.5 - - + -
144D TYR* 4.0 20.0 - + - -
145D ARG* 3.5 4.2 - - - +
146D SER* 3.0 43.8 + - - +
170D GLU* 5.2 1.1 - - - -
301D A9S 3.8 24.9 - - + -
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Residues in contact with ARG 133 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118D GLU* 3.3 2.6 - - - -
119D ILE* 2.9 34.8 + - + +
121D GLU* 3.3 35.8 + - - +
132D PHE* 1.3 78.3 - - - +
134D VAL* 1.3 71.4 + - - +
135D LEU* 3.8 20.9 - - - -
143D ASN* 4.4 21.8 + - - +
144D TYR 3.6 6.3 - - - +
145D ARG* 3.9 28.8 - - + +
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Residues in contact with VAL 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116D SER* 3.7 17.3 - - - +
117D VAL 3.8 4.7 - - - +
118D GLU* 5.0 2.0 - - + -
132D PHE* 4.2 17.3 - - + -
133D ARG* 1.3 83.7 + - - +
135D LEU* 1.3 62.4 + - - +
136D GLY* 3.5 24.7 - - - +
139D HIS* 3.9 18.6 - - + +
141D LEU 4.2 4.9 - - - +
142D ASN* 5.4 0.9 - - - -
143D ASN* 4.1 20.9 + - - +
144D TYR* 2.8 40.0 + - + +
301D A9S 4.8 5.2 - - + -
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Residues in contact with LEU 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102D ILE* 4.9 4.9 - - + -
117D VAL* 2.9 28.0 + - + +
118D GLU 4.8 0.2 - - - -
119D ILE* 3.4 43.5 - - + +
133D ARG* 3.7 28.5 + - - -
134D VAL* 1.3 74.1 - - - +
136D GLY* 1.3 57.2 + - - +
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Residues in contact with GLY 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117D VAL* 3.1 27.2 + - - +
134D VAL* 3.5 7.7 - - - +
135D LEU* 1.3 79.6 - - - +
137D GLY* 1.3 60.8 + - - -
139D HIS* 3.5 16.4 - - - -
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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