Contacts of the strand formed by residues 10 - 17 (chain D) in PDB entry 5JCZ
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 TYR 10 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8D TYR* 3.3 11.2 - - - -
9D ASP* 1.3 98.6 - - + +
11D LEU* 1.3 60.7 + - - +
12D PHE* 3.7 33.7 - + + -
58D LYS* 4.1 17.5 + - + -
59D THR 3.2 3.0 + - - -
60D ILE* 4.2 13.5 - - + -
61D LYS 2.8 25.6 + - - -
173D TYR* 3.4 31.3 + + - -
176D VAL* 4.5 12.3 - - + -
177D SER* 3.5 30.5 - - - -
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Residues in contact with LEU 11 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D TYR* 3.6 26.8 - - + +
10D TYR* 1.3 73.1 - - - +
12D PHE* 1.3 67.4 + - - +
13D LYS 3.9 2.1 + - - +
61D LYS* 3.4 44.2 - - + +
63D GLN* 4.0 35.0 - - + +
85D VAL* 5.3 0.3 - - - +
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Residues in contact with PHE 12 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D TYR* 3.7 35.9 - + + -
11D LEU* 1.3 80.1 - - - +
13D LYS* 1.3 63.0 + - - +
14D VAL* 3.5 3.6 + - + +
60D ILE* 3.5 38.4 - - + -
61D LYS 3.0 10.5 + - - +
62D ALA* 3.7 2.9 - - - -
63D GLN* 2.9 26.7 + - - -
85D VAL* 3.8 16.4 - - + -
169D LEU* 3.8 28.7 - - + -
172D ILE* 3.6 34.5 - - + -
173D TYR* 3.9 13.7 - - - -
176D VAL* 4.4 14.8 - - + -
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Residues in contact with LYS 13 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1633C ILE 5.4 1.2 + - - -
11D LEU* 3.9 3.8 + - - +
12D PHE* 1.3 70.6 - - - +
14D VAL* 1.3 60.7 + - - +
15D VAL* 4.0 4.7 - - - -
63D GLN* 3.3 15.7 - - - +
65D TRP* 3.4 49.7 - - + +
79D ALA 3.2 13.3 + - - -
80D TYR 3.1 27.5 + - - -
82D ARG 2.6 29.7 + - - +
83D GLY* 3.9 12.5 + - - +
84D ALA* 3.5 12.9 - - + +
85D VAL* 2.9 31.6 + - - +
86D GLY 3.4 4.7 + - - -
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Residues in contact with VAL 14 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D PHE 4.0 9.4 - - - +
13D LYS* 1.3 79.3 - - - +
15D VAL* 1.3 67.9 + - - +
16D LEU* 4.9 0.4 - - + -
62D ALA* 5.3 0.7 - - + -
63D GLN 2.9 8.5 + - - +
64D ILE* 3.2 21.1 - - + +
65D TRP* 2.7 32.9 + - - +
86D GLY* 3.3 24.2 - - - +
87D ALA* 4.1 4.0 - - - +
88D LEU* 4.5 14.6 - - + +
165D PHE* 5.0 8.7 - - + -
168D ILE* 4.8 7.6 - - + -
169D LEU* 4.0 23.8 - - + -
172D ILE* 4.4 6.1 - - + -
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Residues in contact with VAL 15 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13D LYS* 4.0 3.4 - - - -
14D VAL* 1.3 77.5 - - - +
16D LEU* 1.3 64.8 + - - +
17D ILE* 4.3 4.7 - - + -
65D TRP* 3.7 18.2 - - + -
80D TYR* 3.3 39.5 - - + +
81D TYR* 4.2 24.7 - - + -
84D ALA* 3.9 17.0 - - + -
86D GLY 3.0 5.6 + - - +
87D ALA* 3.7 20.5 - - + +
88D LEU 3.0 24.8 + - - -
117D ILE* 5.0 0.2 - - + -
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Residues in contact with LEU 16 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D VAL* 4.9 1.3 - - + -
15D VAL* 1.3 78.2 - - - +
17D ILE* 1.3 66.1 + - - +
24D LYS* 3.2 49.2 - - + +
27D LEU* 5.3 2.5 - - + -
28D LEU* 3.8 25.6 - - + +
64D ILE* 3.9 14.4 - - + -
65D TRP 3.1 18.9 + - - +
66D ASP* 3.9 13.2 - - - +
67D THR* 4.6 4.2 - - - +
80D TYR* 2.7 21.5 + - - -
88D LEU* 3.9 33.4 - - + +
90D VAL* 5.4 2.9 - - + -
165D PHE* 4.4 5.4 - - + -
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Residues in contact with ILE 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D VAL* 4.1 5.8 + - + -
16D LEU* 1.3 79.7 - - - +
18D GLY* 1.3 59.3 + - - +
24D LYS* 3.5 11.2 - - - +
80D TYR* 4.2 9.4 - - + -
81D TYR* 3.3 33.4 - - + +
87D ALA* 4.8 5.6 - - + -
88D LEU 3.1 13.0 + - - +
89D LEU* 3.7 27.6 - - + -
90D VAL* 2.9 26.3 + - - +
105D TRP* 4.0 23.6 - - + +
108D GLU* 4.8 0.9 - - - +
109D LEU* 3.8 26.7 - - + -
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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