Contacts of the strand formed by residues 78 - 85 (chain S) in PDB entry 2ZJP
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 PRO 78 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19S ILE* 4.7 23.4 - - + +
36S ARG* 6.3 0.4 - - + -
39S PHE* 4.7 18.8 - - + -
40S ASP* 5.2 9.2 - - - +
69S VAL* 4.6 17.3 - - + -
71S MET* 3.1 19.3 - - + -
72S ASP* 4.2 1.7 - - - +
76S ARG 4.1 3.4 - - - +
77S ALA* 1.3 93.8 - - + +
79S ILE* 1.3 62.9 + - - +
80S HIS 5.0 0.2 - - - +
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Residues in contact with ILE 79 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14S LEU* 6.4 2.9 - - + -
19S ILE* 3.8 7.8 - - - +
20S ALA* 3.6 27.1 + - + +
70S GLN* 2.6 30.7 + - + +
71S MET 4.1 8.1 - - - +
72S ASP* 4.1 11.4 - - + +
78S PRO* 1.3 77.2 - - - +
80S HIS* 1.3 64.3 + - + +
78Z A 3.7 11.7 - - - +
79Z U 3.6 36.6 - - - +
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Residues in contact with HIS 80 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20S ALA 2.8 22.9 + - - -
21S ALA* 4.2 1.1 - - - -
22S VAL* 3.5 16.3 - - + +
68S ALA 5.1 0.4 - - - -
69S VAL* 3.2 5.5 - - - +
70S GLN* 2.6 45.2 + - + +
79S ILE* 1.3 82.8 - - + +
81S VAL* 1.3 64.0 + - - +
82S ASP* 2.9 27.8 + - - -
77Z G 3.0 57.7 + - - -
78Z A 3.0 36.9 + - - +
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Residues in contact with VAL 81 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19S ILE* 3.8 20.4 - - + -
20S ALA 3.6 4.0 + - - -
21S ALA* 3.4 31.3 - - + +
22S VAL 3.6 2.1 + - - -
34S LEU* 5.7 0.2 - - + -
39S PHE* 3.4 38.1 - - + -
66S VAL* 4.1 7.6 - - + -
68S ALA 3.8 1.3 - - - -
69S VAL* 3.1 40.8 - - + -
78S PRO* 5.2 1.3 - - + -
80S HIS* 1.3 83.3 + - - +
82S ASP* 1.3 71.7 + - - +
83S PHE* 4.1 7.0 - - + -
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Residues in contact with ASP 82 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22S VAL* 4.0 9.4 - - - +
24S TYR* 4.8 11.8 + - + +
66S VAL* 3.6 1.8 - - - +
67S LYS* 2.6 41.8 + - + +
68S ALA* 2.7 39.5 + - + +
80S HIS* 2.9 21.9 + - - -
81S VAL* 1.3 86.6 - - - +
83S PHE* 1.3 57.9 + - - +
77Z G 3.4 19.4 + - - -
105Z G 3.6 14.0 + - - -
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Residues in contact with PHE 83 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1S MET* 3.3 31.9 - - + -
3S LEU* 6.1 1.6 - - + -
21S ALA* 3.4 33.0 - - + -
22S VAL 3.3 8.7 + - - +
23S ALA* 3.0 42.2 - - + -
24S TYR* 3.3 9.2 + - - -
32S PHE* 6.0 1.6 - + - -
34S LEU* 3.3 28.5 - - + -
39S PHE* 4.0 11.9 - + - -
54S ILE* 4.0 17.3 - - + -
64S ALA* 4.1 11.2 - - + -
65S LEU 3.9 3.1 - - - -
66S VAL* 4.7 19.5 - - + -
67S LYS* 4.4 0.4 - - - +
81S VAL* 4.1 13.2 - - + -
82S ASP* 1.3 75.5 - - - +
84S TYR* 1.3 59.0 + - - +
85S MET 3.8 0.4 - - - -
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Residues in contact with TYR 84 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24S TYR* 3.4 22.9 - + + -
25S ASN* 3.6 28.6 + - + +
65S LEU* 2.7 46.3 + - + +
67S LYS* 4.0 22.0 - - + -
82S ASP 3.7 0.6 + - - -
83S PHE* 1.3 71.2 - - - +
85S MET* 1.3 74.2 + - - +
87S THR* 4.8 3.0 + - - -
91S PRO* 3.1 33.3 + - + -
92S VAL* 3.7 21.0 - - + +
106Z U 5.5 0.4 - - - -
107Z C 3.3 24.8 + - - -
108Z G 2.9 26.5 + - - -
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Residues in contact with MET 85 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23S ALA* 3.7 15.5 - - + -
24S TYR* 3.2 19.0 + - - +
25S ASN* 3.5 30.8 - - + +
28S ASN* 5.3 7.0 - - - +
32S PHE* 5.0 2.2 - - + -
54S ILE* 3.4 22.4 - - + -
62S PHE* 3.4 33.0 - - + -
63S PRO* 2.6 34.3 - - + +
64S ALA* 3.2 25.8 - - + +
83S PHE 3.8 1.6 - - - -
84S TYR* 1.3 92.5 - - - +
86S VAL* 1.3 71.1 + - - +
87S THR* 4.1 1.2 + - - -
91S PRO* 5.4 0.7 - - - +
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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