Contacts of the strand formed by residues 129 - 136 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B ILE* 4.9 4.3 - - + -
40B HIS* 3.7 41.7 - - + +
66B TRP* 3.2 5.6 - - - -
122B VAL* 3.3 16.1 - - + +
124B ASP* 3.1 35.4 + - + +
127B LYS* 3.5 29.2 - - + +
128B ARG* 1.3 82.5 - - - +
130B LEU* 1.3 67.1 + - - +
147B VAL* 4.0 15.9 - - + -
148B THR 3.2 13.9 - - - +
149B SER* 3.8 14.4 - - - -
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Residues in contact with LEU 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B TRP* 3.6 5.0 - - + -
69B VAL* 3.0 42.4 - - + +
70B ARG* 3.8 19.7 - - - +
72B PHE* 4.6 12.1 - - + +
103B ARG* 5.3 2.0 - - - +
120B LEU* 3.8 22.2 - - + -
122B VAL 3.1 5.2 - - - +
123B LEU* 4.5 6.3 - - + -
129B ILE* 1.3 78.2 - - - +
131B SER* 1.3 89.5 + - - +
132B PHE* 4.2 16.6 - - + +
147B VAL* 3.6 1.0 - - - -
148B THR* 2.9 37.6 + - - +
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Residues in contact with SER 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120B LEU* 3.4 5.5 - - - +
121B GLU* 2.9 33.2 + - - +
122B VAL* 2.9 33.5 + - - +
130B LEU* 1.3 81.0 - - - +
132B PHE* 1.3 63.1 + - - +
145B ARG* 5.8 0.9 - - - +
146B SER 2.6 22.4 + - - -
147B VAL* 3.4 18.7 - - - +
148B THR* 5.9 0.2 - - - -
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Residues in contact with PHE 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B PHE* 4.0 14.8 - - + -
79B LYS* 4.0 20.0 - - - -
103B ARG* 4.1 15.9 - - - -
116B SER* 5.9 0.4 - - - -
118B GLU* 3.4 28.9 - - + -
119B ILE 3.3 15.5 - - - +
121B GLU* 4.5 4.3 - - - +
130B LEU* 4.3 11.2 - - + -
131B SER* 1.3 77.8 + - - +
133B ARG* 1.3 61.8 + - - +
134B VAL* 4.1 16.8 - - + -
144B TYR* 3.9 19.5 - + - -
145B ARG* 3.4 3.3 - - - +
146B SER* 3.0 46.4 + - - +
148B THR* 6.0 1.1 - - - -
170B GLU* 6.2 0.9 - - - -
301B A9S 4.1 20.6 - - + -
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Residues in contact with ARG 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B GLU* 3.2 2.9 - - - -
119B ILE* 2.9 36.3 + - + +
121B GLU* 3.5 28.0 - - - +
132B PHE* 1.3 78.7 - - - +
134B VAL* 1.3 68.2 + - - +
135B LEU* 4.6 4.7 - - + -
144B TYR 3.5 7.0 - - - +
145B ARG* 4.2 8.7 - - + +
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Residues in contact with VAL 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B SER* 3.8 15.0 - - - +
117B VAL 3.4 6.3 - - - +
118B GLU* 4.3 1.3 - - + +
132B PHE* 4.1 12.3 - - + -
133B ARG* 1.3 77.1 - - - +
135B LEU* 1.3 67.5 + - - +
136B GLY* 3.5 23.1 - - - +
139B HIS* 3.7 23.3 - - + +
141B LEU 4.5 2.2 - - - +
142B ASN* 5.5 0.9 - - - +
143B ASN* 4.1 21.0 + - - +
144B TYR* 2.8 47.2 + - + +
301B A9S 4.9 4.3 - - + -
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Residues in contact with LEU 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B ILE* 5.3 4.3 - - + -
117B VAL* 2.7 28.3 + - + +
118B GLU 4.8 0.2 - - - -
119B ILE* 3.6 51.1 - - + +
133B ARG* 3.9 6.0 + - + +
134B VAL* 1.3 80.8 - - - +
136B GLY* 1.3 57.2 + - - +
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Residues in contact with GLY 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B VAL* 3.1 27.9 + - - +
134B VAL* 3.5 6.2 - - - +
135B LEU* 1.3 81.7 - - - +
137B GLY* 1.3 62.4 + - - -
139B HIS* 3.3 14.9 - - - -
142B ASN* 5.4 7.4 - - - -
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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