Contacts of the strand formed by residues 129 - 136 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A ILE* 5.1 4.0 - - + -
40A HIS* 3.7 44.4 - - + +
66A TRP* 3.4 3.7 - - - -
122A VAL* 3.6 20.9 - - + +
123A LEU* 3.7 0.9 - - - -
124A ASP* 3.2 33.0 + - + -
127A LYS* 3.4 31.4 - - + +
128A ARG* 1.3 79.5 - - - +
130A LEU* 1.3 66.2 + - - +
147A VAL* 4.1 17.3 - - + -
148A THR 3.1 10.1 - - - +
149A SER* 3.9 14.1 - - - -
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Residues in contact with LEU 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A TRP* 3.9 6.1 - - + -
69A VAL* 3.1 41.1 - - + +
70A ARG* 3.9 15.7 - - - +
72A PHE* 4.5 19.5 - - + -
103A ARG* 5.9 0.2 - - - +
120A LEU* 4.2 8.3 - - + -
122A VAL 3.5 8.7 - - - +
123A LEU* 4.4 9.6 - - + +
129A ILE* 1.3 78.0 - - - +
131A SER* 1.3 87.4 + - - +
132A PHE* 4.0 20.2 - - + -
147A VAL* 3.4 0.5 - - - -
148A THR* 2.6 46.3 + - - +
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Residues in contact with SER 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A LEU* 3.4 6.4 - - - +
121A GLU* 2.9 31.2 + - - +
122A VAL* 3.1 32.7 + - - +
130A LEU* 1.3 82.8 - - - +
132A PHE* 1.3 64.0 + - - +
145A ARG* 5.4 2.8 - - - +
146A SER 2.7 20.9 + - - -
147A VAL* 3.5 19.7 - - - +
148A THR* 5.6 0.2 - - - -
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Residues in contact with PHE 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A PHE* 4.1 13.9 - - + -
79A LYS* 4.0 3.1 - - - -
103A ARG* 3.9 20.0 - - - -
118A GLU* 3.6 23.8 - - + -
119A ILE 3.2 18.6 - - - +
121A GLU* 4.2 2.9 - - - +
130A LEU* 4.0 15.7 - - + -
131A SER* 1.3 76.8 + - - +
133A ARG* 1.3 64.4 + - - +
134A VAL* 4.3 7.0 - - + -
144A TYR* 3.9 19.3 - + - -
145A ARG* 3.1 19.4 - - - +
146A SER* 3.2 36.1 + - - +
148A THR* 5.7 3.1 - - - -
170A GLU* 6.1 0.9 - - - -
301A A9S 3.5 34.1 - - + -
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Residues in contact with ARG 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A GLU* 3.2 1.6 - - - -
119A ILE* 2.7 41.1 + - + +
121A GLU* 3.0 37.5 + - - +
132A PHE* 1.3 78.1 - - - +
134A VAL* 1.3 73.7 + - - +
135A LEU* 3.5 17.1 + - + -
143A ASN* 5.7 2.5 - - - -
144A TYR 3.6 8.1 - - - +
145A ARG* 3.7 37.7 - - + +
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Residues in contact with VAL 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A SER* 3.6 18.8 - - - +
117A VAL 3.6 3.6 - - - +
118A GLU* 4.3 1.6 - - + +
132A PHE* 4.3 11.0 - - + -
133A ARG* 1.3 78.9 - - - +
135A LEU* 1.3 60.2 + - - +
136A GLY* 3.4 27.8 - - - +
139A HIS* 3.8 13.5 - - - +
141A LEU 4.5 4.0 - - - +
142A ASN* 5.3 0.7 - - - -
143A ASN* 4.2 20.3 + - - +
144A TYR* 2.7 51.1 + - + +
301A A9S 4.7 7.9 - - + -
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Residues in contact with LEU 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A ILE* 4.1 20.6 - - + -
117A VAL* 2.7 26.7 + - + +
119A ILE* 3.5 49.1 - - + +
133A ARG* 3.5 17.9 + - + -
134A VAL* 1.3 77.0 - - - +
136A GLY* 1.3 54.8 + - - +
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Residues in contact with GLY 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A VAL* 3.0 30.5 + - - +
134A VAL* 3.4 8.2 - - - +
135A LEU* 1.3 79.8 - - - +
137A GLY* 1.3 58.7 + - - -
139A HIS* 3.3 15.4 - - - -
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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