Contacts of the strand formed by residues 31 - 37 (chain S) in PDB entry 1ZGL
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 SER 31 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77H THR* 5.5 1.4 - - - +
29S TYR 4.7 1.0 + - - -
30S PRO* 1.3 71.3 - - - +
32S LEU* 1.3 71.8 + - - +
33S PHE* 4.1 10.3 - - - -
48S LYS* 5.9 0.4 - - - -
49S ALA 3.3 9.0 - - - -
50S THR* 2.8 35.9 + - - +
92S LEU* 3.2 4.9 - - - +
93S SER* 2.6 40.0 + - - +
101T ASN* 5.4 6.4 + - - -
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Residues in contact with LEU 32 (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* 3.3 31.6 - - + -
30S PRO* 4.4 2.7 - - + -
31S SER* 1.3 84.1 - - - +
33S PHE* 1.3 76.4 + - - +
49S ALA 2.6 32.0 + - - +
66S TYR* 3.4 41.7 - - + -
73S PHE* 3.2 50.3 - - + -
90S CYS* 5.5 2.5 - - - -
91S ALA 3.3 9.9 - - - +
92S LEU* 4.1 7.6 - - + -
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Residues in contact with PHE 33 (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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31S SER* 4.1 9.9 - - - -
32S LEU* 1.3 86.4 - - - +
34S TRP* 1.3 67.6 + - - +
35S TYR* 4.3 27.4 - - + -
45S LEU* 4.5 6.7 - - + -
47S LEU 3.1 11.0 - - - +
48S LYS* 3.4 36.6 - - + -
73S PHE* 3.0 19.4 - - - -
90S CYS* 4.2 0.2 - - - -
91S ALA* 2.7 39.2 + - + +
92S LEU 4.0 1.1 - - - -
93S SER* 2.9 39.7 - - - -
104S LEU* 4.3 7.2 - - + -
102T THR 3.8 12.1 - - - -
103T GLU* 4.1 16.6 - - - -
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Residues in contact with TRP 34 (chain S).
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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5S GLN* 3.6 9.2 - - - -
20S ILE* 3.4 26.7 - - + -
21S ASN 4.3 1.3 - - - -
22S CYS* 4.0 5.6 - - + -
33S PHE* 1.3 84.3 - - - +
35S TYR* 1.3 58.5 + - - +
46S LEU* 2.5 40.7 + - - +
47S LEU* 3.1 18.9 + - + +
64S ALA* 3.8 9.6 - - + +
73S PHE* 2.7 44.8 + + - -
75S LEU* 3.1 50.4 - - + +
88S TYR* 3.7 20.2 - + + -
89S PHE 3.2 26.2 - - - -
90S CYS* 3.5 34.5 - - + -
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Residues in contact with TYR 35 (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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33S PHE* 4.3 16.8 - - + -
34S TRP* 1.3 79.4 - - - +
36S VAL* 1.3 59.3 + - - +
37S GLN 4.3 0.2 - - - -
43S LEU* 4.1 23.3 - - + -
44S GLN 3.0 21.5 - - - +
45S LEU* 3.4 32.0 - - + +
88S TYR* 3.6 5.2 - - - +
89S PHE* 2.8 41.8 + - + -
91S ALA* 4.4 5.2 - - + -
104S LEU* 3.0 27.4 - - + +
106S PHE* 3.2 40.6 - + - -
103T GLU 3.1 14.4 + - - -
106T ALA* 3.3 14.6 + - + +
107T PHE* 5.7 0.9 - - - -
108T PHE* 4.7 7.9 - + - -
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Residues in contact with VAL 36 (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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35S TYR* 1.3 74.7 - - - +
37S GLN* 1.3 62.3 + - - +
38S TYR* 3.4 44.0 + - + +
42S GLY 3.7 0.9 - - - +
43S LEU* 4.6 1.1 - - - -
44S GLN* 2.7 54.7 + - + +
45S LEU 4.1 1.6 - - - +
46S LEU* 3.6 32.8 - - + -
86S ALA* 3.9 6.3 - - + -
87S VAL 3.4 11.2 - - - +
88S TYR* 3.9 13.2 - - + -
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Residues in contact with GLN 37 (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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36S VAL* 1.3 72.5 - - - +
38S TYR* 1.3 72.8 + - - +
41S GLU 3.7 23.3 + - - +
42S GLY* 3.5 11.3 - - - +
43S LEU* 3.1 23.6 - - + +
86S ALA* 3.9 3.0 - - - -
87S VAL* 2.9 39.9 + - + +
89S PHE* 4.2 10.7 - - + -
37T GLN* 2.5 47.2 + - - +
91T LEU* 4.8 1.4 - - - +
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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