Contacts of the strand formed by residues 165 - 170 (chain A) in PDB entry 5MR9
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 165 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A CYS* 2.0 54.1 - - + -
104A GLY 4.2 0.2 - - - -
130A CYS* 3.9 13.8 - - - +
131A ALA* 3.7 28.3 - - - -
132A GLY 4.4 9.2 - - - +
134A CYS* 3.6 12.9 - - - -
164A CYS* 1.3 68.5 - - - +
166A ARG* 1.3 63.5 + - - +
195A ALA 3.5 5.4 - - - -
160B ARG* 3.7 20.9 + - + +
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Residues in contact with ARG 166 (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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130A CYS* 3.7 7.0 - - - -
164A CYS* 3.2 16.5 + - + +
165A CYS* 1.3 76.9 - - - +
167A PRO* 1.4 78.9 - - + +
168A THR* 3.5 2.8 + - - +
170A TYR* 3.7 14.5 + - - -
195A ALA* 3.1 29.1 + - - +
197A VAL* 4.4 5.4 - - + +
139B ARG* 5.0 2.2 - - - +
141B TYR* 4.0 5.8 - - - -
142B ASP* 2.7 38.8 + - - -
160B ARG* 2.9 33.7 + - + -
162B GLN 3.4 22.0 + - - +
163B PRO* 4.1 4.9 - - - +
164B CYS* 4.8 1.1 - - - -
197B VAL* 2.8 58.0 + - + +
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Residues in contact with PRO 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A CYS* 3.5 8.0 - - - -
166A ARG* 1.4 99.9 - - + +
168A THR* 1.3 61.5 + - - +
169A ALA 3.8 5.6 - - - +
170A TYR* 3.5 40.7 + - + +
191A ALA* 3.7 12.3 - - + -
193A GLU 3.2 14.8 - - - +
197A VAL* 5.7 0.5 - - - +
141B TYR* 3.5 34.5 - - + +
197B VAL* 4.7 7.8 - - - +
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Residues in contact with THR 168 (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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166A ARG 3.5 2.9 + - - +
167A PRO* 1.3 74.6 - - - +
169A ALA* 1.3 59.5 + - - +
170A TYR* 5.3 2.2 - - - -
193A GLU* 3.0 28.1 + - - +
194A CYS 4.0 3.8 + - - -
195A ALA* 3.5 28.8 - - + +
197A VAL* 4.6 13.2 - - + -
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Residues in contact with ALA 169 (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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167A PRO* 3.4 2.7 - - - +
168A THR* 1.3 81.5 + - - +
170A TYR* 1.3 64.1 + - - +
191A ALA* 3.6 5.5 - - - -
192A ARG* 2.8 39.5 + - + -
193A GLU* 3.4 30.0 + - + +
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Residues in contact with TYR 170 (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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166A ARG* 3.7 14.6 + - - -
167A PRO* 3.5 39.9 + - + +
168A THR 5.3 0.9 - - - -
169A ALA* 1.3 79.4 - - - +
171A GLU* 1.3 64.7 + - - +
172A ASP* 3.5 2.4 + - - -
188A GLU* 3.7 42.7 + - + +
190A SER 3.4 17.0 - - - +
191A ALA* 4.4 0.2 - - - -
192A ARG* 3.7 14.9 + - - +
139B ARG* 3.4 45.2 + - - -
141B TYR* 3.7 27.9 - + + -
197B VAL 4.2 5.1 + - - -
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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