Contacts of the strand formed by residues 133 - 143 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139A THR 4.5 0.2 - - - -
140A ARG* 3.4 5.9 - - - +
141A LYS* 3.1 45.8 + - + +
143A THR* 6.0 2.7 - - - -
126B GLU* 3.8 32.5 - - + +
127B ARG* 3.4 7.6 - - - -
128B GLN* 3.5 48.0 + - + -
132B GLY* 1.3 74.9 - - - -
134B ILE* 1.3 58.9 + - - +
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Residues in contact with ILE 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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138A PHE* 3.9 19.1 - - + -
139A THR 3.2 24.9 - - - +
140A ARG* 3.7 24.2 - - + +
124B HIS* 3.5 8.7 - - + -
126B GLU* 3.3 5.7 - - - +
127B ARG* 3.0 35.2 + - + +
129B ASP* 3.7 30.1 - - + +
133B TYR* 1.3 77.1 - - - +
135B SER* 1.3 74.2 + - - +
136B ARG* 3.8 30.5 - - + +
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Residues in contact with SER 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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137A CYS* 6.1 0.4 - - - -
138A PHE* 3.2 5.6 - - - -
139A THR* 3.0 46.2 + - - -
124B HIS* 3.7 17.3 - - - -
125B GLU* 4.0 1.1 - - - -
126B GLU* 3.8 20.2 + - - +
134B ILE* 1.3 77.9 - - - +
136B ARG* 1.3 62.2 + - - +
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Residues in contact with ARG 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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137A CYS* 3.5 8.1 - - - +
138A PHE* 4.5 6.5 - - + +
140A ARG* 3.6 23.4 - - - +
103B HIS* 3.5 53.2 + - - +
104B PHE* 3.8 14.8 - - + -
123B LYS* 3.4 3.5 - - - +
124B HIS* 3.2 70.0 + - + +
127B ARG* 5.9 0.4 - - - +
129B ASP* 3.7 10.7 + - - +
134B ILE* 3.8 21.3 - - + +
135B SER* 1.3 78.9 - - - +
137B CYS* 1.3 63.3 + - - +
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Residues in contact with CYS 137 (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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136A ARG* 3.4 1.9 - - - +
137A CYS* 2.0 78.8 + - - +
104B PHE* 4.9 1.1 - - - -
122B GLY 3.3 11.9 - - - +
123B LYS* 4.4 16.4 - - + -
136B ARG* 1.3 77.0 - - - +
138B PHE* 1.3 66.3 + - - +
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Residues in contact with PHE 138 (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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134A ILE* 4.2 10.5 - - + -
135A SER* 3.2 14.6 - - - +
136A ARG* 4.4 7.0 - - + -
99B LEU* 4.4 6.5 - - + -
101B VAL* 3.9 21.5 - - + -
104B PHE* 3.5 42.8 - + - -
109B LEU* 4.2 7.9 - - + -
120B ILE* 4.0 23.6 - - + -
121B THR* 3.5 2.9 - - - +
122B GLY* 3.0 50.2 + - - +
137B CYS* 1.3 77.9 - - - +
139B THR* 1.3 75.3 + - - +
140B ARG* 4.0 14.8 - - + -
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Residues in contact with THR 139 (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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126A GLU* 5.7 1.6 - - - +
133A TYR 4.0 0.5 - - - +
134A ILE* 3.3 4.9 - - - +
135A SER* 2.9 45.5 + - - -
119B GLU* 4.0 30.5 - - + +
120B ILE 3.4 5.8 - - - +
121B THR* 4.1 13.0 + - - +
138B PHE* 1.3 78.8 + - - +
140B ARG* 1.3 62.4 + - - +
141B LYS* 4.5 14.3 - - + +
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Residues in contact with ARG 140 (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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129A ASP* 2.9 42.4 + - - -
131A HIS* 3.7 20.5 - - - +
132A GLY* 4.0 2.6 - - - +
133A TYR 3.4 10.7 + - - -
134A ILE* 3.9 28.2 - - + +
136A ARG* 4.2 8.3 - - - +
99B LEU* 4.1 29.5 - - + +
118B VAL 3.8 0.3 - - - +
119B GLU* 3.5 2.8 - - - +
120B ILE* 2.7 47.9 + - + +
138B PHE* 4.0 15.9 - - + -
139B THR* 1.3 74.9 - - - +
141B LYS* 1.3 66.8 + - - +
142B TYR* 3.6 33.4 - - + -
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Residues in contact with LYS 141 (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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126A GLU* 3.2 29.1 + - - +
132A GLY* 3.7 7.1 - - - -
133A TYR* 3.0 41.0 + - + +
201A GOL 3.2 28.3 + - - +
117B VAL* 4.2 13.0 - - + -
118B VAL 3.2 7.2 - - - +
119B GLU* 3.5 34.4 + - + +
139B THR* 4.5 11.9 - - + -
140B ARG* 1.3 83.6 - - - +
142B TYR* 1.3 65.5 + - - +
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Residues in contact with TYR 142 (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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131A HIS* 3.7 35.7 - - + +
132A GLY* 5.4 1.3 - - - -
88B ILE* 4.8 7.4 - - + +
95B TRP* 4.0 25.4 - + + -
97B VAL* 4.1 34.6 - - + +
98B SER 4.2 6.9 + - - -
99B LEU* 3.9 28.9 - - - +
117B VAL* 3.4 8.3 - - - +
118B VAL* 3.0 41.5 + - + +
120B ILE* 3.7 23.6 - - + -
140B ARG* 3.6 27.2 + - + -
141B LYS* 1.3 75.5 - - - +
143B THR* 1.3 63.3 + - - +
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Residues in contact with THR 143 (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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133A TYR* 4.8 10.5 - - + -
201A GOL 3.7 30.5 - - - +
95B TRP* 4.3 12.6 + - - -
116B GLY 4.1 4.3 - - - +
117B VAL* 4.3 7.4 - - + -
142B TYR* 1.3 76.2 - - - +
144B LEU* 1.3 65.8 + - - +
145B PRO* 4.2 0.3 - - - +
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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