Contacts of the strand formed by residues 147 - 154 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138A GLY* 4.1 10.5 - - - +
141A ASP* 2.9 16.6 - - + -
142A ALA 5.2 0.4 - - - +
146A GLY* 1.3 72.6 - - - -
148A ARG* 1.3 72.8 + - - +
149A THR 3.5 0.5 + - - -
164A VAL* 2.9 1.8 - - - -
165A LEU* 2.6 62.2 + - + +
74B ILE* 4.0 15.3 - - + +
75B ALA 5.3 0.2 - - - -
76B LEU* 4.3 33.0 - - + +
86B ILE* 3.4 8.3 - - + +
401B NAG 5.1 6.1 - - + -
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Residues in contact with ARG 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A GLU* 3.0 26.8 + - - -
126A ALA* 3.4 14.5 + - - +
127A SER* 3.4 18.7 + - - +
128A THR 5.8 0.2 + - - -
134A ASP 4.5 5.9 + - - -
135A CYS* 4.8 0.9 - - - -
136A LYS* 3.8 11.4 - - - +
137A ARG* 3.3 6.4 - - - +
138A GLY 2.8 26.7 + - - -
140A ASN* 2.6 59.5 + - + +
141A ASP* 2.9 18.5 - - + +
143A ARG* 5.1 7.5 - - - +
147A VAL* 1.3 74.3 - - - +
149A THR* 1.3 60.5 + - - +
162A CYS* 2.9 44.2 - - - -
163A GLU 3.4 4.7 - - - +
164A VAL* 3.3 14.8 - - + -
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Residues in contact with THR 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A LYS* 5.0 3.6 - - + -
135A CYS* 4.0 5.0 - - - +
137A ARG* 3.9 26.4 + - - +
147A VAL 3.5 2.6 + - - -
148A ARG* 1.3 75.3 - - - +
150A GLY* 1.3 67.7 + - - +
151A ARG* 2.8 18.9 + - - +
163A GLU* 3.0 52.7 + - + +
164A VAL* 4.4 2.5 - - - +
165A LEU* 4.8 14.3 - - + +
401B NAG 6.1 0.2 - - - -
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Residues in contact with GLY 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A HIS* 3.6 12.5 - - - +
135A CYS* 2.9 40.0 - - - +
137A ARG* 3.7 23.2 - - - +
149A THR* 1.3 74.8 + - - +
151A ARG* 1.3 56.3 + - - +
152A CYS 3.6 0.2 + - - -
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Residues in contact with ARG 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A HIS* 4.6 11.2 - - + -
135A CYS* 3.4 3.6 - - - -
149A THR* 2.8 18.6 + - - +
150A GLY* 1.3 76.9 - - - +
152A CYS* 1.3 61.1 + - - +
153A VAL* 4.2 3.8 - - + -
163A GLU* 3.1 43.8 + - + +
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Residues in contact with CYS 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A CYS* 2.0 46.2 - - - -
130A THR 4.6 0.7 - - - -
131A SER* 3.6 35.4 - - - +
132A HIS* 3.8 19.7 + - + +
135A CYS* 3.7 7.6 - - - -
150A GLY 3.6 1.0 + - - -
151A ARG* 1.3 74.3 - - - +
153A VAL* 1.3 70.6 + - - +
160A LYS* 4.6 6.5 - - - -
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Residues in contact with VAL 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A CYS* 4.6 0.7 - - - -
120A ALA* 4.0 20.2 - - + +
151A ARG* 5.1 2.9 - - + -
152A CYS* 1.3 81.1 - - - +
154A SER* 1.3 58.1 + - - +
160A LYS* 3.4 6.0 - - - +
161A THR 2.5 48.8 + - - +
163A GLU* 3.5 42.4 - - + +
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Residues in contact with SER 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A ALA* 4.0 7.4 - - - +
153A VAL* 1.3 75.9 - - - +
155A TYR* 1.3 62.5 + - - +
156A SER* 3.2 21.8 + - - -
157A ALA* 5.4 0.9 - - - -
159A VAL 3.6 6.7 - - - -
160A LYS* 3.7 8.2 - - - +
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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