Contacts of the strand formed by residues 133 - 143 (chain D) in PDB entry 6GJH
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 TYR 133 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113B THR 4.6 0.2 + - - -
150B PRO* 3.6 30.6 - - - +
151B THR* 3.8 38.2 + - + +
140C ARG* 3.6 3.5 - - - +
141C LYS* 3.2 39.4 + - + +
126D GLU* 3.9 30.7 - - + +
127D ARG* 3.3 11.9 - - - -
128D GLN* 3.2 49.8 + - + -
132D GLY* 1.3 73.9 - - - -
134D ILE* 1.3 61.4 + - - +
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Residues in contact with ILE 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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138C PHE* 4.2 19.3 - - + -
139C THR 3.3 15.3 - - - +
140C ARG* 3.2 32.8 - - + +
124D HIS* 3.3 9.7 - - + -
126D GLU* 4.1 3.8 - - - +
127D ARG 2.8 37.8 + - - +
129D ASP* 3.6 26.5 - - + +
133D TYR* 1.3 76.7 - - - +
135D SER* 1.3 71.1 + - - +
136D ARG* 3.7 33.7 - - + +
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Residues in contact with SER 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138C PHE* 3.2 8.4 - - - +
139C THR* 3.0 45.2 + - - -
124D HIS* 3.5 17.9 - - - -
125D GLU* 3.9 1.6 - - - -
126D GLU* 3.8 22.9 + - - +
134D ILE* 1.3 74.5 - - - +
136D ARG* 1.3 64.5 + - - +
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Residues in contact with ARG 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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137C CYS* 3.5 7.9 - - - +
138C PHE* 4.4 6.3 - - + +
140C ARG* 3.7 11.1 - - - +
103D HIS* 3.4 50.2 + - - +
104D PHE* 3.9 16.4 - - + -
123D LYS* 3.5 3.1 - - - +
124D HIS* 3.2 59.3 + - - +
129D ASP* 3.0 26.7 + - - +
130D GLU* 5.2 0.4 + - - -
134D ILE* 3.7 26.0 - - + +
135D SER* 1.3 80.0 - - - +
137D CYS* 1.3 64.3 + - - +
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Residues in contact with CYS 137 (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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135C SER 6.2 0.2 - - - -
136C ARG* 3.5 2.2 - - - +
137C CYS* 2.0 77.6 + - - +
104D PHE* 4.8 0.7 - - - -
122D GLY 3.3 12.1 - - - +
123D LYS* 4.4 14.6 - - + -
136D ARG* 1.3 76.8 - - - +
138D PHE* 1.3 67.4 + - - +
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Residues in contact with PHE 138 (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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134C ILE* 4.3 14.1 - - + -
135C SER* 3.1 15.0 - - - +
136C ARG* 4.4 7.0 - - + +
99D LEU* 4.2 19.1 - - + -
101D VAL* 3.8 24.0 - - + -
104D PHE* 3.6 37.0 - + - -
109D LEU* 4.3 7.4 - - + -
120D ILE* 3.8 20.0 - - + -
121D THR* 3.4 3.8 - - - -
122D GLY* 3.1 49.0 + - - +
137D CYS* 1.3 79.5 - - - +
139D THR* 1.3 76.0 + - - +
140D ARG* 4.3 4.0 - - + -
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Residues in contact with THR 139 (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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126C GLU* 5.3 4.1 - - - +
133C TYR 4.4 0.3 - - - -
134C ILE* 3.3 6.1 - - - +
135C SER* 2.9 44.6 + - - -
119D GLU* 3.9 32.5 - - + +
120D ILE 3.3 5.2 - - - -
121D THR* 3.5 14.8 - - + +
138D PHE* 1.3 79.1 + - - +
140D ARG* 1.3 64.5 + - - +
141D LYS* 4.7 11.2 - - + +
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Residues in contact with ARG 140 (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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129C ASP* 3.2 38.4 + - - -
131C HIS* 3.9 16.3 - - - +
132C GLY 4.0 4.4 - - - +
133C TYR 3.2 10.0 + - - +
134C ILE* 3.6 32.9 - - + +
136C ARG* 4.0 10.9 - - - +
86D SER* 3.4 10.3 + - - -
99D LEU* 4.1 18.0 - - + +
118D VAL 3.8 0.3 - - - +
119D GLU* 3.5 3.5 - - - +
120D ILE* 2.8 41.5 + - + +
138D PHE* 4.1 9.4 - - + -
139D THR* 1.3 75.4 - - - +
141D LYS* 1.3 67.1 + - - +
142D TYR* 3.2 35.8 - - + -
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Residues in contact with LYS 141 (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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126C GLU* 2.8 35.5 + - - +
132C GLY* 3.5 8.0 - - - -
133C TYR* 3.1 39.6 + - + +
117D VAL* 3.9 17.0 - - + -
118D VAL 3.2 9.6 - - - +
119D GLU* 4.2 27.8 + - + -
139D THR* 4.7 6.7 - - + +
140D ARG* 1.3 80.0 - - - +
142D TYR* 1.3 65.4 + - - +
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Residues in contact with TYR 142 (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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131C HIS* 3.9 31.4 - - + -
132C GLY* 5.3 2.0 - - - -
86D SER* 2.3 39.9 + - - -
88D ILE* 5.1 2.9 - - + -
95D TRP* 4.0 23.6 - + + -
97D VAL* 4.2 32.7 - - + +
99D LEU* 4.3 6.8 - - - +
117D VAL* 3.3 8.1 - - - +
118D VAL* 3.0 40.9 + - + +
120D ILE* 3.8 28.9 - - + -
140D ARG* 3.2 20.4 - - + -
141D LYS* 1.3 77.2 - - - +
143D THR* 1.3 61.2 + - - +
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Residues in contact with THR 143 (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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133C TYR* 5.9 3.3 - - - -
95D TRP* 4.2 14.1 + - - -
116D GLY 3.8 10.8 - - - +
117D VAL* 4.7 7.3 - - + +
142D TYR* 1.3 72.9 - - - +
144D LEU* 1.3 74.8 + - - +
145D PRO* 4.0 0.9 - - - +
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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