Contacts of the strand formed by residues 130 - 138 (chain D) in PDB entry 3BDW
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 CYS 130 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118D HIS* 3.9 7.9 - - - -
119D CYS* 2.0 53.2 - - + -
120D PRO* 4.4 0.4 - - + -
123D TRP* 3.8 19.5 - - + -
124D ILE 3.2 6.1 - - - -
129D SER* 1.3 73.7 - - - +
131D TYR* 1.3 65.3 + - - +
230D LYS* 3.3 8.8 - - - +
231D HIS* 3.2 46.0 + - + +
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Residues in contact with TYR 131 (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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123D TRP* 3.1 13.0 - - - +
124D ILE* 2.7 58.2 + - + +
126D TYR* 3.7 32.0 - + + -
127D SER* 5.8 0.2 - - - -
129D SER* 3.6 27.6 + - - -
130D CYS* 1.3 79.6 - - - +
132D TYR* 1.3 59.8 + - - +
133D ILE* 4.0 6.8 + - + +
155D LEU* 4.2 9.2 - - + -
162D GLU* 2.8 32.5 + - + +
165D PHE* 4.9 2.0 - + - -
166D LEU* 3.9 28.5 - - + -
228D HIS* 5.7 3.4 - - + -
229D CYS 3.4 11.7 - - - -
230D LYS* 3.6 26.8 - - + -
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Residues in contact with TYR 132 (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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122D GLU* 4.0 26.1 - - + +
123D TRP* 3.4 48.0 - + + +
131D TYR* 1.3 73.4 - - - +
133D ILE* 1.3 66.3 + - - +
134D GLY* 3.4 32.9 + - - -
136D GLU* 5.2 4.7 + - - -
150D LYS* 3.3 38.8 + - + -
227D TYR* 5.3 0.9 - + - -
228D HIS* 3.2 28.6 - - - +
229D CYS* 3.1 20.2 + - + -
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Residues in contact with ILE 133 (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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107C PHE* 3.7 14.8 - - + +
110C SER* 5.7 0.9 - - - +
124D ILE* 3.4 37.5 - - + -
131D TYR* 4.2 9.0 - - + +
132D TYR* 1.3 77.6 - - - +
134D GLY* 1.3 62.2 + - - +
135D LYS* 2.7 51.1 + - + +
166D LEU* 5.9 3.6 - - + -
169D ILE* 3.6 21.3 - - + +
170D SER* 3.1 24.9 - - - +
226D ILE* 5.9 0.2 - - + -
228D HIS* 3.5 18.4 - - + +
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Residues in contact with GLY 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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132D TYR* 3.4 30.0 + - - -
133D ILE* 1.3 71.1 - - - +
135D LYS* 1.3 65.0 + - - +
136D GLU* 3.2 20.6 + - - +
227D TYR* 3.5 19.7 - - - -
228D HIS* 3.4 13.1 - - - -
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Residues in contact with LYS 135 (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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106C ASP* 3.5 41.6 + - - +
107C PHE* 3.9 6.6 - - - +
109C SER* 3.5 14.8 - - - +
110C SER* 5.8 3.8 - - - +
133D ILE* 2.7 45.6 + - + +
134D GLY* 1.3 73.2 - - - +
136D GLU* 1.3 61.6 + - - +
137D ARG 4.4 0.2 + - - -
226D ILE* 3.6 26.6 - - + +
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Residues in contact with GLU 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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145B LEU* 3.5 35.3 - - - +
132D TYR* 5.2 3.6 + - - -
134D GLY 3.2 11.0 + - - +
135D LYS* 1.3 81.9 - - + +
137D ARG* 1.3 65.3 - - - +
138D ARG* 4.5 12.9 + - - +
150D LYS* 4.8 6.4 + - - -
226D ILE* 3.8 7.5 - - - +
227D TYR* 3.2 42.0 + - + +
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Residues in contact with ARG 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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135D LYS 4.4 0.2 + - - -
136D GLU* 1.3 73.5 - - - +
138D ARG* 1.3 71.5 + - - +
224D SER* 3.9 28.3 + - - -
225D ILE* 3.4 12.3 - - - +
226D ILE* 3.7 31.2 - - + +
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Residues in contact with ARG 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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138B ARG* 5.9 6.8 - - - +
142B GLU* 4.3 31.4 + - - +
145B LEU* 4.4 24.4 - - - +
136D GLU* 4.2 14.1 + - - +
137D ARG* 1.3 83.9 + - - +
139D THR* 1.3 59.8 + - - +
142D GLU* 3.4 36.0 + - + -
143D SER* 3.4 17.9 - - - +
146D ALA* 4.7 5.9 - - - +
174D TRP* 2.9 13.5 + - - -
223D SER 3.4 0.2 - - - +
224D SER* 3.8 7.2 - - - +
225D ILE 2.8 26.2 + - - +
227D TYR* 3.5 34.1 + - + -
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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