Contacts of the strand formed by residues 70 - 79 (chain A) in PDB entry 1CJY
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 70 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A LEU 4.2 0.4 - - - +
26A ARG* 3.4 26.5 - - + -
63A PHE* 3.5 19.1 - - - -
68A ASN 4.0 6.9 + - - +
69A PRO* 1.3 72.6 - - - +
71A TRP* 1.3 61.4 + - - +
72A ASN* 3.4 29.6 - - - +
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Residues in contact with TRP 71 (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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24A VAL* 3.3 30.5 - - + +
25A LEU 2.6 7.4 + - - -
26A ARG* 3.7 35.4 - - - -
27A ALA* 3.9 11.4 - - + -
44A PRO* 3.8 11.8 + - + -
45A TYR* 3.7 23.6 - - - -
46A VAL* 3.4 21.5 - - + -
60A THR* 3.1 15.9 + - - -
61A ARG 3.0 30.2 + - - -
63A PHE* 3.6 21.0 - + - -
69A PRO* 3.8 24.9 - - + -
70A VAL* 1.3 73.4 - - - +
72A ASN* 1.3 73.1 + - - +
73A GLU* 3.4 20.0 - - + +
91A LEU* 4.1 8.3 - - + -
130A MET* 4.5 2.9 - - + -
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Residues in contact with ASN 72 (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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23A VAL* 4.6 4.9 - - + -
24A VAL 2.6 15.5 + - - -
25A LEU* 2.9 50.1 + - + +
26A ARG* 5.2 1.6 - - - +
70A VAL* 3.4 22.0 - - + +
71A TRP* 1.3 76.0 - - - +
73A GLU* 1.3 58.1 + - - +
74A THR* 4.4 1.8 + - - -
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Residues in contact with GLU 73 (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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22A VAL 3.5 1.2 - - - +
23A VAL* 3.2 3.2 - - - -
24A VAL 2.7 35.9 + - - +
59A ARG 4.3 1.0 - - - +
60A THR* 3.2 23.3 - - + -
61A ARG* 3.2 37.7 + - - +
63A PHE* 6.1 0.5 - - - -
71A TRP* 3.7 19.5 - - + +
72A ASN* 1.3 81.5 - - - +
74A THR* 1.3 63.0 + - - +
75A PHE* 3.4 24.2 - - + -
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Residues in contact with THR 74 (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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21A THR* 3.4 29.8 - - + -
22A VAL 3.3 4.7 - - - +
23A VAL* 3.7 16.9 - - + +
72A ASN 5.1 1.9 + - - -
73A GLU* 1.3 74.5 - - - +
75A PHE* 1.3 75.6 + - - +
76A GLU* 4.5 8.7 + - + +
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Residues in contact with PHE 75 (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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21A THR* 3.5 2.4 - - - +
22A VAL* 2.7 46.3 + - - +
24A VAL* 3.7 16.6 - - + -
48A LEU* 3.7 31.0 - - + -
58A LYS* 3.8 27.4 - - + -
59A ARG* 3.9 15.3 - - - -
60A THR* 3.9 16.8 - - + -
73A GLU* 3.4 46.7 - - + -
74A THR* 1.3 78.9 - - - +
76A GLU* 1.3 63.4 + - - +
77A PHE* 3.9 9.6 - - + -
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Residues in contact with GLU 76 (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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19A LYS* 4.0 27.7 + - + +
20A PHE 3.9 3.8 - - - -
21A THR* 3.5 25.4 + - + +
58A LYS* 3.5 19.8 + - - +
74A THR* 4.9 7.2 - - + +
75A PHE* 1.3 77.0 - - - +
77A PHE* 1.3 69.5 + - - +
78A ILE* 5.0 7.0 - - + -
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Residues in contact with PHE 77 (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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18A HIS 3.6 0.2 - - - +
19A LYS* 3.4 5.7 - - - +
20A PHE* 2.9 48.1 + + + +
22A VAL* 4.2 9.0 - - + -
48A LEU* 3.9 29.8 - - + -
50A ILE* 3.3 35.9 - - + -
53A THR* 5.5 3.8 - - + -
56A SER* 3.2 40.6 - - - -
58A LYS* 3.7 22.4 - - + +
75A PHE* 3.9 21.3 - - + -
76A GLU* 1.3 78.9 - - - +
78A ILE* 1.3 66.4 + - - +
79A LEU* 4.1 9.4 - - + -
87A LEU* 4.5 1.6 - - + -
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Residues in contact with ILE 78 (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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17A SER* 4.5 17.5 - - - +
18A HIS 3.4 7.2 - - - +
19A LYS* 5.0 17.0 - - + -
53A THR* 3.1 28.5 + - + +
76A GLU* 5.0 5.6 - - + +
77A PHE* 1.3 84.3 - - - +
79A LEU* 1.3 60.7 + - - +
139A CYS* 5.3 6.5 - - + -
373A PHE* 3.3 36.7 - - + +
374A MET* 4.8 0.7 - - - -
376A THR* 3.9 27.6 - - + -
377A VAL 5.1 2.9 - - - +
378A VAL* 4.5 19.4 - - + +
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Residues in contact with LEU 79 (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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17A SER* 3.5 6.8 - - - -
18A HIS* 2.8 45.3 + - + +
20A PHE* 3.5 40.8 - - + -
50A ILE* 3.9 23.8 - - + -
53A THR* 3.5 15.0 - - - +
77A PHE* 4.1 6.5 - - + +
78A ILE* 1.3 76.6 - - - +
80A ASP* 1.3 60.6 + - - +
81A PRO* 3.6 0.3 - - - +
85A ASN* 2.8 42.2 - - + +
109A VAL* 4.0 12.3 - - + -
136A LEU* 4.9 2.9 - - + -
374A MET* 4.4 4.3 - - - -
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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