Contacts of the strand formed by residues 129 - 136 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36C ILE* 5.7 4.3 - - + -
40C HIS* 4.7 15.7 - - + -
66C TRP* 3.2 7.8 - - - -
122C VAL* 4.0 15.0 - - + +
123C LEU* 3.8 0.5 - - - -
124C ASP* 3.0 37.1 + - + -
127C LYS* 3.8 27.1 - - + +
128C ARG* 1.3 81.1 - - - +
130C LEU* 1.3 64.5 + - - +
131C SER* 5.3 0.2 - - - -
147C VAL* 3.7 23.3 - - + -
148C THR 3.2 10.8 - - - +
149C SER* 4.2 12.1 - - - -
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Residues in contact with LEU 130 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C TRP* 3.9 14.5 - - + -
69C VAL* 4.1 24.7 - - + +
70C ARG* 4.9 2.9 - - - +
72C PHE* 4.7 9.0 - - + -
103C ARG* 6.1 0.4 - - - +
120C LEU* 3.7 21.3 - - + -
122C VAL 3.3 10.8 - - - +
123C LEU* 4.6 11.0 - - + -
129C ILE* 1.3 77.0 - - - +
131C SER* 1.3 78.9 + - - +
132C PHE* 4.7 13.2 - - + -
146C SER* 5.5 0.2 + - - -
147C VAL* 3.3 1.6 - - - +
148C THR* 2.4 48.0 + - - +
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Residues in contact with SER 131 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120C LEU* 3.5 5.4 - - - +
121C GLU* 2.8 30.0 + - - +
122C VAL* 3.0 33.6 + - - +
129C ILE* 5.3 0.2 - - - -
130C LEU* 1.3 80.4 - - - +
132C PHE* 1.3 63.6 + - - +
145C ARG* 4.9 5.7 - - - +
146C SER* 2.6 20.8 + - - -
147C VAL* 3.5 18.9 - - - +
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Residues in contact with PHE 132 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72C PHE* 4.2 16.6 - - + -
79C LYS* 3.9 4.7 - - - -
103C ARG* 3.6 22.4 - - - -
118C GLU* 3.6 28.0 - - + -
119C ILE 3.4 13.2 - - - +
121C GLU* 4.2 4.0 - - - +
130C LEU* 4.7 11.7 - - + -
131C SER* 1.3 77.0 + - - +
133C ARG* 1.3 61.1 + - - +
134C VAL* 3.9 17.9 - - + -
144C TYR* 3.8 19.1 - + - -
145C ARG* 3.4 3.6 - - - -
146C SER* 3.0 50.1 + - - -
170C GLU* 5.6 0.2 - - - -
301C A9S 3.9 26.2 - - + -
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Residues in contact with ARG 133 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118C GLU* 3.1 2.8 - - - -
119C ILE* 2.8 39.6 + - + +
121C GLU* 3.1 29.9 + - - +
132C PHE* 1.3 77.8 - - - +
134C VAL* 1.3 71.6 + - - +
135C LEU* 3.3 26.0 - - - +
143C ASN* 5.3 9.0 + - - +
144C TYR 3.5 7.9 - - - +
145C ARG* 3.7 28.7 - - + +
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Residues in contact with VAL 134 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116C SER* 3.9 13.9 - - - +
117C VAL 3.6 5.4 - - - +
118C GLU* 4.2 2.5 - - + +
132C PHE* 3.9 19.5 - - + -
133C ARG* 1.3 88.5 + - - +
135C LEU* 1.3 63.4 + - - +
136C GLY 3.5 24.0 - - - +
139C HIS* 3.7 20.4 - - + +
141C LEU 4.4 3.6 - - - +
142C ASN* 5.5 1.1 - - - +
143C ASN* 4.3 17.3 + - - +
144C TYR* 2.7 42.5 + - + +
301C A9S 5.1 4.5 - - + -
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Residues in contact with LEU 135 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102C ILE* 4.1 19.3 - - + -
117C VAL* 2.8 24.4 + - + +
119C ILE* 3.8 44.0 - - + +
133C ARG* 3.3 30.7 - - - +
134C VAL* 1.3 76.0 - - - +
136C GLY* 1.3 57.6 + - - +
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Residues in contact with GLY 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117C VAL* 3.1 27.9 + - - +
134C VAL* 3.5 6.4 - - - +
135C LEU* 1.3 80.8 - - - +
137C GLY* 1.3 62.0 + - - -
139C HIS* 3.2 16.6 - - - -
142C ASN* 5.6 6.1 - - - -
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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