Contacts of the strand formed by residues 137 - 143 (chain A) in PDB entry 3BRW
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 THR 137 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84A ASN* 5.7 3.1 - - - +
86A THR* 4.1 21.3 + - - +
87A ALA* 6.4 0.2 - - - -
130A LEU* 4.6 13.0 - - - +
131A LEU 3.3 7.2 + - - -
132A ARG* 3.4 26.3 - - - +
133A THR* 4.7 0.2 - - - -
136A ARG* 1.3 103.7 + - - +
138A TYR* 1.3 63.0 + - - +
139A HIS* 3.9 2.4 + - - +
185A ASP* 4.6 6.9 + - - +
390A ARG* 3.6 17.7 - - - +
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Residues in contact with TYR 138 (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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109A LEU* 5.9 2.4 - - + +
129A LEU 4.0 0.2 - - - +
130A LEU* 3.4 5.4 - - - +
131A LEU* 2.6 47.5 + - + +
133A THR* 3.7 25.0 - - + +
136A ARG* 3.8 32.4 - - + +
137A THR* 1.3 71.6 - - - +
139A HIS* 1.3 60.2 + - - +
160A VAL* 3.7 25.7 - - + +
161A CYS* 3.5 35.0 - - + -
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Residues in contact with HIS 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A THR* 5.3 3.4 - - - +
89A ILE* 3.6 23.7 - - + +
128A ARG* 3.3 36.4 + - + +
129A LEU 3.1 22.9 - - - -
130A LEU* 3.5 21.8 - - + -
137A THR 3.9 4.0 + - - +
138A TYR* 1.3 75.1 - - - +
140A ASP* 1.3 71.1 + - - +
141A VAL* 4.3 4.6 - - + +
160A VAL* 3.7 3.0 - - - +
121D GLU* 3.2 51.7 + - + +
122D ASP* 5.3 0.2 - - - -
124D ARG* 4.3 15.3 + - + -
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Residues in contact with ASP 140 (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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127A LEU 4.0 0.2 - - - +
129A LEU* 3.1 31.9 + - - +
139A HIS* 1.3 85.3 - - - +
141A VAL* 1.3 81.9 + - - +
142A ILE* 3.9 7.8 + - + +
159A LEU 5.0 4.0 - - - +
160A VAL* 3.5 19.9 - - + +
124D ARG* 3.9 6.2 + - - +
127D GLY* 3.2 2.8 - - - -
128D LYS* 2.8 34.8 + - - +
129D GLU* 3.5 27.7 + - - +
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Residues in contact with VAL 141 (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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126A HIS* 3.4 35.0 - - + +
127A LEU 4.1 2.5 - - - -
128A ARG* 3.7 22.2 - - + +
139A HIS* 4.3 2.7 - - - +
140A ASP* 1.3 85.7 + - - +
142A ILE* 1.3 66.4 + - - +
143A PRO* 4.0 3.3 - - - +
124D ARG* 3.6 36.7 - - + +
125D VAL 3.4 22.2 - - - +
127D GLY* 3.1 28.9 + - - +
129D GLU* 5.2 1.0 + - - +
130D GLN* 4.7 3.2 + - - +
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Residues in contact with ILE 142 (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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126A HIS* 4.2 2.0 - - - -
127A LEU* 2.8 52.0 + - + +
129A LEU* 3.4 31.2 - - + -
140A ASP* 4.5 11.2 - - - +
141A VAL* 1.3 79.3 - - - +
143A PRO* 1.3 80.9 - - + +
144A ILE* 5.5 4.7 - - + -
151A PRO* 6.4 0.9 - - + -
159A LEU* 3.5 45.5 - - + +
160A VAL* 5.1 0.7 - - + -
129D GLU* 5.6 7.6 - - + -
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Residues in contact with PRO 143 (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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125A GLU 3.5 9.6 - - - +
126A HIS* 3.9 5.8 - - + -
141A VAL 4.0 1.3 - - - +
142A ILE* 1.3 99.9 - - + +
144A ILE* 1.3 66.3 + - - +
147A LEU* 5.2 1.7 - - - +
87D GLN* 5.4 4.3 - - - +
129D GLU* 6.1 1.8 - - + -
130D GLN* 3.4 48.7 - - + +
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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