Contacts of the strand formed by residues 47 - 54 (chain X) in PDB entry 3RCI
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 LEU 47 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45X ASN 3.5 4.6 + - - +
46X PRO* 1.3 75.4 - - - +
48X VAL* 1.3 57.0 + - - +
63X VAL* 4.5 14.6 - - + -
64X LEU 3.4 3.4 - - - +
65X GLU* 3.8 31.9 - - + -
175X ILE* 4.0 20.9 - - + -
205X GLN* 3.5 3.6 - - - +
206X LEU* 2.7 43.9 + - + -
207X SER* 2.9 30.2 + - - +
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Residues in contact with VAL 48 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46X PRO* 4.7 1.8 - - + -
47X LEU* 1.3 78.6 - - - +
49X TYR* 1.3 62.3 + - - +
63X VAL* 3.3 9.0 - - - +
64X LEU* 2.8 49.0 + - + +
66X LEU* 3.9 23.8 - - + -
78X PHE* 3.7 29.8 - - + -
79X ARG* 4.2 21.8 - - + -
82X CYS* 3.9 8.3 - - + -
204X GLY 3.2 15.3 - - - +
205X GLN* 4.1 9.0 - - + +
206X LEU* 4.3 1.8 - - - +
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Residues in contact with TYR 49 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48X VAL* 1.3 75.9 - - - +
50X LEU* 1.3 66.6 + - - +
51X ASP* 3.7 14.4 - - - -
61X ARG* 3.5 52.0 - - + -
62X VAL 3.2 6.7 - - - +
63X VAL* 4.6 0.4 - - + -
64X LEU* 5.8 0.2 - - - -
82X CYS* 4.5 1.4 - - - -
202X ASP* 3.0 19.3 + - - -
203X CYS* 3.1 46.9 + - - +
204X GLY* 2.9 40.2 + - - +
205X GLN 3.9 4.3 - - - -
206X LEU* 3.6 32.1 - - + -
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Residues in contact with LEU 50 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49X TYR* 1.3 82.4 - - - +
51X ASP* 1.3 63.6 + - - +
52X VAL* 3.9 13.4 + - + +
61X ARG* 3.4 2.1 - - - -
62X VAL* 2.8 42.5 + - + +
64X LEU* 4.0 22.7 - - + -
78X PHE* 4.7 4.9 - - + -
82X CYS* 4.1 16.4 - - - -
90X TYR* 4.8 5.2 - - + -
95X PHE* 4.3 15.3 - - + -
154X PHE* 4.0 26.7 - - + -
156X ILE* 4.7 6.3 - - + -
200X ILE* 4.2 20.0 - - + -
202X ASP 3.7 4.0 - - - -
203X CYS* 3.8 14.1 - - + -
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Residues in contact with ASP 51 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49X TYR* 3.7 8.8 - - - -
50X LEU* 1.3 71.0 - - - +
52X VAL* 1.3 60.5 + - - +
60X GLY 3.5 6.1 - - - +
61X ARG* 2.8 55.9 + - - +
200X ILE* 3.3 5.2 - - - -
201X THR* 2.8 40.4 + - - +
202X ASP* 2.8 23.3 + - + +
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Residues in contact with VAL 52 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50X LEU* 3.9 19.1 - - + +
51X ASP* 1.3 78.5 - - - +
53X ASP* 1.3 60.1 + - - +
58X PRO* 3.8 1.7 - - - +
59X LEU* 2.8 38.7 + - + +
60X GLY 3.1 12.1 + - - +
62X VAL* 4.6 4.3 - - + -
95X PHE* 4.2 18.8 - - + -
180X VAL* 4.4 10.1 - - + -
184X ILE* 3.9 18.4 - - + -
198X ILE* 3.4 33.2 - - + -
199X VAL 3.2 9.4 - - - +
200X ILE* 4.6 2.5 - - + -
201X THR* 4.9 0.4 - - - -
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Residues in contact with ASP 53 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52X VAL* 1.3 79.3 - - - +
54X ALA* 1.3 60.3 + - - +
55X ASN 4.2 0.4 - - - -
56X GLY* 3.5 35.0 - - - +
57X LYS 3.2 4.3 - - - +
58X PRO* 3.2 22.9 - - - +
59X LEU* 4.2 2.5 - - - -
197X LYS 4.2 0.4 - - - +
198X ILE* 3.3 4.7 - - - +
199X VAL* 2.8 36.4 + - + +
201X THR* 3.2 31.1 + - + +
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Residues in contact with ALA 54 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53X ASP* 1.3 72.6 - - - +
55X ASN* 1.3 72.3 + - - +
57X LYS* 2.9 25.6 + - + +
59X LEU* 3.9 15.7 - - + +
187X PHE* 3.7 33.0 - - + -
196X LYS* 4.1 16.6 + - + +
197X LYS 3.4 5.4 - - - -
198X ILE* 4.8 2.9 - - + -
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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