Contacts of the strand formed by residues 126 - 133 (chain A) in PDB entry 1RC9
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 ARG 126 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A MET* 5.4 0.9 - - - -
40A GLU* 3.5 16.6 + - + -
42A TYR* 3.6 66.9 + - + -
69A GLU* 4.7 3.4 + - - +
71A ILE* 5.8 6.1 - - - +
124A SER 3.5 1.3 - - - -
125A TYR* 1.3 123.3 + - + +
127A ILE* 1.3 61.4 + - - +
146A GLN 3.8 0.2 - - - +
147A TYR* 3.4 6.6 - - - +
148A CYS* 2.9 42.8 + - + +
184A THR* 6.1 0.8 - - - +
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Residues in contact with ILE 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ILE* 4.0 4.0 - - + -
19A VAL* 4.1 22.4 - - + -
22A HIS* 3.4 38.8 - - + +
39A MET* 4.4 17.7 - - + -
40A GLU 3.1 12.6 + - - +
41A TRP* 3.4 9.2 - - + -
42A TYR* 2.8 31.6 + - - +
45A ALA* 4.9 0.2 - - - -
126A ARG* 1.3 76.4 - - - +
128A GLY* 1.3 59.9 + - - +
129A CYS* 3.9 22.4 - - - -
145A CYS* 4.1 2.5 - - + -
146A GLN 3.4 11.2 - - - +
147A TYR* 3.6 18.4 - - + +
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Residues in contact with GLY 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A TRP* 4.0 7.6 - - - -
42A TYR 3.9 3.1 - - - -
45A ALA* 3.7 4.4 - - - +
46A ALA* 3.5 27.1 - - - -
49A ALA* 3.9 4.9 - - - +
127A ILE* 1.3 77.9 - - - +
129A CYS* 1.3 62.5 + - - -
145A CYS* 3.4 0.5 - - - -
146A GLN* 2.8 30.3 + - - +
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Residues in contact with CYS 129 (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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9A PRO* 3.7 13.5 - - + +
18A ILE* 4.0 19.1 - - + -
41A TRP* 3.2 15.9 - - + -
46A ALA* 3.9 15.1 - - - +
49A ALA* 4.0 3.8 - - - -
50A GLU* 4.5 3.6 - - - +
86A TRP* 3.7 13.2 - - + -
127A ILE* 3.9 13.5 - - - -
128A GLY* 1.3 76.4 - - - -
130A ALA* 1.3 64.9 + - - +
144A VAL 3.1 6.5 - - - +
145A CYS* 2.0 47.6 - - - -
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Residues in contact with ALA 130 (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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9A PRO* 3.6 8.7 - - - -
49A ALA* 3.6 7.4 - - + +
50A GLU* 3.4 48.5 - - + +
53A ALA* 4.0 8.5 - - + -
54A TYR* 4.6 2.2 - - + -
86A TRP* 3.6 5.3 - - - -
129A CYS* 1.3 75.2 - - - +
131A ALA* 1.3 61.6 + - - +
143A PHE* 3.6 2.4 - - - -
144A VAL 2.8 30.2 + - - +
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Residues in contact with ALA 131 (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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4A PHE* 3.8 27.5 - - + -
7A GLU 5.1 1.8 - - - +
8A SER* 5.4 1.3 - - - -
9A PRO* 3.8 23.5 - - + +
53A ALA* 4.9 0.7 - - - -
54A TYR* 3.3 19.9 + - - -
86A TRP* 4.1 2.2 - - + +
130A ALA* 1.3 76.4 - - - +
132A ALA* 1.3 59.8 + - - +
142A PHE 3.5 5.4 - - - -
143A PHE* 3.9 17.5 - - + -
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Residues in contact with ALA 132 (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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4A PHE* 3.8 10.2 - - - -
53A ALA* 3.4 27.8 - - + +
54A TYR* 3.8 18.4 - - + -
56A CYS* 4.6 1.1 - - - -
131A ALA* 1.3 76.6 - - - +
133A TYR* 1.3 60.1 - - - +
134A CYS* 3.8 10.0 + - - -
141A TYR* 3.5 5.4 - - - +
142A PHE* 2.9 35.2 + - + +
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Residues in contact with TYR 133 (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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4A PHE* 3.9 18.3 - - + -
56A CYS* 3.9 5.0 - - - -
132A ALA* 1.3 72.8 - - - +
134A CYS* 1.3 61.0 + - - +
135A PRO* 3.4 40.8 - - + +
140A SER* 3.3 29.1 + - - -
141A TYR* 3.5 31.0 - + + -
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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