Contacts of the strand formed by residues 147 - 153 (chain B) in PDB entry 3I5D
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 VAL 147 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138B GLY* 4.2 10.1 - - - +
141B ASP* 2.9 17.7 - - + -
146B GLY* 1.3 72.0 - - - -
148B ARG* 1.3 74.6 + - - +
149B THR 3.5 0.3 + - - -
164B VAL* 2.9 1.1 - - - -
165B LEU* 2.6 62.6 + - + +
74C ILE* 4.3 9.0 - - + +
75C ALA* 5.7 0.4 - - - -
76C LEU* 4.0 39.9 - - + +
86C ILE* 3.1 12.5 - - + +
184C ASP* 5.9 0.2 - - - +
401C NAG 5.1 4.9 - - + -
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Residues in contact with ARG 148 (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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136B LYS 3.7 9.0 - - - +
137B ARG* 3.3 2.1 - - - +
138B GLY 2.9 27.4 + - - -
140B ASN* 3.6 19.5 - - + -
141B ASP* 2.9 29.0 - - - +
147B VAL* 1.3 76.3 - - - +
149B THR* 1.3 62.3 + - - +
162B CYS* 4.9 5.6 - - + -
163B GLU 3.3 12.6 - - - +
164B VAL* 3.6 8.1 - - + -
401C NAG 5.6 1.6 - - - +
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Residues in contact with THR 149 (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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118B LYS* 3.9 25.7 - - + -
135B CYS* 4.0 6.1 - - - +
137B ARG* 4.2 4.7 - - - -
147B VAL 3.5 2.4 + - - -
148B ARG* 1.3 76.1 - - - +
150B GLY* 1.3 68.2 + - - +
151B ARG* 2.9 18.3 + - - +
163B GLU* 2.9 56.9 + - + +
164B VAL* 4.4 2.0 - - - +
165B LEU* 4.8 7.0 - - - +
401C NAG 6.4 1.1 - - - -
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Residues in contact with GLY 150 (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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132B HIS* 3.6 11.5 - - - +
135B CYS* 2.9 37.7 - - - +
137B ARG* 3.6 23.2 - - - +
149B THR* 1.3 74.9 + - - +
151B ARG* 1.3 56.3 + - - +
152B CYS 3.6 0.9 + - - -
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Residues in contact with ARG 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B LYS* 5.4 12.2 - - - +
132B HIS* 4.5 15.3 - - + -
135B CYS* 3.7 1.6 - - - -
149B THR* 2.9 15.7 + - - +
150B GLY* 1.3 76.2 - - - +
152B CYS* 1.3 60.5 + - - +
153B VAL* 5.1 3.6 - - + -
163B GLU* 3.2 50.6 + - - +
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Residues in contact with CYS 152 (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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129B CYS* 2.0 44.4 - - - -
130B THR 4.6 0.7 - - - -
131B SER* 3.6 34.1 - - - +
132B HIS* 3.8 20.4 + - + +
135B CYS* 3.7 9.9 - - - -
150B GLY 3.6 1.6 + - - -
151B ARG* 1.3 73.3 - - - +
153B VAL* 1.3 71.3 + - - +
160B LYS* 4.5 6.5 - - - -
161B THR 4.4 0.2 - - - -
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Residues in contact with VAL 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B CYS* 4.6 0.7 - - - -
120B ALA* 4.0 21.3 - - + +
151B ARG* 5.0 3.1 - - + -
152B CYS* 1.3 80.2 - - - +
154B SER* 1.3 57.1 + - - +
160B LYS* 3.5 5.5 - - - +
161B THR 2.5 47.9 + - - +
163B GLU* 3.5 43.3 - - + +
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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