Contacts of the strand formed by residues 41 - 50 (chain C) in PDB entry 4ZIN
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 THR 41 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35C GLY* 3.2 0.8 - - - -
36C ARG* 3.0 46.3 + - - +
39C GLU* 3.7 18.1 + - + +
40C GLY* 1.3 83.6 - - - +
42C GLN* 1.3 64.5 + - - +
72C TYR* 3.8 5.2 + - - -
214C TYR* 3.4 28.9 - - - +
215C GLU 3.4 2.9 - - - -
216C ARG* 4.0 20.4 - - + +
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Residues in contact with GLN 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C PHE* 3.1 17.5 - - + -
34C GLU 3.3 14.4 - - - +
35C GLY* 3.9 1.3 - - - -
41C THR* 1.3 77.5 - - - +
43C THR* 1.3 72.6 + - - +
66C CH6 3.9 19.7 - - + +
69C SER* 2.8 50.5 + - - -
72C TYR* 3.8 25.5 + - + +
214C TYR* 3.4 3.3 - - - -
215C GLU* 2.9 57.6 + - + +
217C ALA* 6.1 0.2 - - - +
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Residues in contact with THR 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C PHE* 4.0 3.3 - - - -
33C GLY* 3.0 3.0 - - - -
34C GLU* 2.8 51.4 + - - +
42C GLN* 1.3 81.8 - - - +
44C ALA* 1.3 61.9 - - - +
45C LYS* 5.4 8.5 - - - -
66C CH6 4.4 2.7 - - - -
202C THR* 6.1 0.4 - - - +
213C GLN 3.3 11.0 - - - +
214C TYR* 3.6 23.6 - - + -
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Residues in contact with ALA 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C PHE* 3.7 16.2 - - + -
32C GLU 3.4 9.4 - - - +
33C GLY* 3.8 0.4 - - - -
43C THR* 1.3 78.8 - - - +
45C LYS* 1.3 64.0 - - - +
46C LEU* 4.1 17.9 - - + +
65C PHE* 5.4 0.4 - - + -
66C CH6 3.3 24.9 - - + -
211C VAL 4.1 0.5 - - - +
212C GLU* 3.3 6.4 - - - +
213C GLN 2.9 32.1 + - - +
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Residues in contact with LYS 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C GLU 4.2 0.2 - - - +
31C GLY* 3.1 3.6 - - - -
32C GLU* 2.8 39.5 + - + +
33C GLY* 6.4 0.2 - - - -
34C GLU* 5.7 3.6 + - - -
43C THR* 5.4 9.0 - - - -
44C ALA* 1.3 73.6 - - - +
46C LEU* 1.3 62.5 + - - +
47C LYS* 5.4 9.0 - - - +
210C ILE* 6.0 3.4 - - + -
211C VAL 3.6 4.3 - - - +
212C GLU* 3.6 41.6 + - + +
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Residues in contact with LEU 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C VAL* 3.9 19.1 - - + -
29C ILE* 3.9 10.3 - - + -
30C GLU 3.8 1.8 - - - -
31C GLY* 3.9 3.6 - - - +
44C ALA* 4.2 15.3 - - + +
45C LYS* 1.3 82.8 - - - +
47C LYS* 1.3 64.6 + - - +
58C TRP* 3.9 21.8 - - + -
65C PHE* 3.8 34.3 - - + -
209C THR 4.5 0.2 - - - -
210C ILE* 3.4 6.2 - - - +
211C VAL* 2.7 39.8 + - - +
213C GLN* 3.6 39.3 - - + +
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Residues in contact with LYS 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C ILE* 3.2 4.9 - - - -
30C GLU* 2.9 39.3 + - + +
32C GLU* 5.9 0.4 + - - -
45C LYS* 5.4 8.2 + - - +
46C LEU* 1.3 78.1 - - - +
48C VAL* 1.3 65.5 + - - +
49C THR* 3.2 12.7 + - + +
58C TRP* 6.1 0.2 - - - -
209C THR 3.2 9.2 - - - +
210C ILE* 4.4 30.1 - - + +
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Residues in contact with VAL 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C PHE* 5.0 0.2 - - + -
28C GLU 3.5 6.1 - - - +
29C ILE* 4.1 10.5 - - + -
47C LYS* 1.3 72.5 - - - +
49C THR* 1.3 60.9 + - - +
50C LYS 3.5 21.8 - - - +
52C GLY* 3.6 25.1 + - - +
54C LEU* 4.1 28.5 - - + -
58C TRP* 4.3 6.7 - - + -
208C TYR 3.7 9.0 - - - +
209C THR* 2.9 39.1 + - + +
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Residues in contact with THR 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C GLU* 2.9 25.9 + - - +
30C GLU* 3.6 44.6 + - + +
47C LYS* 3.2 19.3 + - + +
48C VAL* 1.3 74.0 - - - +
50C LYS* 1.3 67.6 + - - +
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Residues in contact with LYS 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C PHE* 3.4 7.4 - - - +
28C GLU* 3.1 63.8 + - + +
48C VAL* 3.5 6.5 - - - +
49C THR* 1.3 86.0 + - - +
51C GLY* 1.3 62.5 + - - +
52C GLY 3.3 3.8 + - - -
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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