Contacts of the strand formed by residues 33 - 40 (chain C) in PDB entry 4ZM0
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 ARG 33 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29C THR* 5.8 0.2 - - - -
30C ARG* 3.1 63.1 + - + +
31C ARG 3.3 15.5 - - - +
32C GLY* 1.3 79.9 - - - +
34C GLU* 1.3 67.4 + - - +
35C PRO* 3.6 2.9 - - - +
18D ASN* 3.1 24.0 + - - +
21D GLU* 3.0 25.5 + - - +
4F G 5.6 0.7 - - - -
5F T 4.5 7.9 - - - -
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Residues in contact with GLU 34 (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 ILE 5.1 0.3 - - - +
30C ARG* 4.9 8.8 + - - -
32C GLY 5.7 0.9 - - - +
33C ARG* 1.3 78.6 - - - +
35C PRO* 1.3 81.0 - - + +
36C ALA* 3.9 2.3 + - - +
21D GLU* 3.5 39.7 + - + +
40D SER* 6.4 1.3 - - - -
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Residues in contact with PRO 35 (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 GLU* 3.5 34.3 - - + +
28C ILE 3.9 4.7 - - - +
29C THR* 4.3 13.5 - - + -
33C ARG 3.6 4.7 - - - +
34C GLU* 1.3 102.4 - - + +
36C ALA* 1.3 59.0 + - - +
40D SER* 4.0 5.5 - - - -
41D LYS* 3.2 33.2 + - + +
42D ALA 4.9 0.2 + - - -
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Residues in contact with ALA 36 (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 GLU* 3.3 8.8 - - - +
28C ILE* 2.9 38.9 + - + +
34C GLU 3.9 2.0 + - - +
35C PRO* 1.3 74.8 - - - +
37C VAL* 1.3 63.5 + - - +
17D LEU* 5.3 12.8 - - + +
20D VAL* 3.9 21.8 - - + -
38D ILE* 5.6 3.8 - - + -
39D VAL 3.5 12.3 - - - +
40D SER* 4.3 0.4 - - - -
41D LYS* 3.7 4.5 - - - +
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Residues in contact with VAL 37 (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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1C MET* 4.3 11.4 - - - -
25C GLU* 4.3 12.8 - - + -
26C VAL 3.3 22.7 - - - +
27C GLU* 4.5 2.5 - - + -
28C ILE* 4.5 0.9 - - - +
36C ALA* 1.3 76.8 - - - +
38C ILE* 1.3 71.1 + - - +
39C VAL* 3.8 4.6 + - + -
37D VAL 3.5 2.4 - - - +
38D ILE* 3.4 3.1 - - - -
39D VAL* 2.8 46.5 + - + +
41D LYS* 3.9 12.8 - - + -
44D PHE* 3.6 40.2 - - + -
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Residues in contact with ILE 38 (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* 5.0 7.4 - - + -
17C LEU* 6.4 0.4 - - - -
20C VAL* 3.3 23.5 - - + +
25C GLU* 4.0 0.7 - - - -
26C VAL* 2.9 35.5 + - + +
28C ILE* 5.1 5.7 - - + +
37C VAL* 1.3 71.9 - - - +
39C VAL* 1.3 60.4 + - - +
36D ALA* 5.5 3.8 - - + -
37D VAL 3.4 8.1 - - - +
38D ILE* 4.3 9.6 - - + +
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Residues in contact with VAL 39 (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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20C VAL* 3.5 8.0 - - - +
24C GLU 4.8 2.0 - - - +
25C GLU* 3.8 24.9 - - + -
37C VAL* 4.5 6.1 - - + +
38C ILE* 1.3 73.5 - - - +
40C SER* 1.4 70.2 + - - +
43C THR* 4.1 16.2 - - + -
44C PHE* 3.9 21.8 - - + +
36D ALA* 3.4 1.1 - - - +
37D VAL* 2.8 43.2 + - + +
39D VAL* 4.4 6.1 - - + -
44D PHE* 3.9 33.9 - - + -
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Residues in contact with SER 40 (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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20C VAL* 3.3 30.8 + - - +
21C GLU* 4.7 11.0 + - - +
23C GLY* 5.5 3.1 - - - -
24C GLU 5.0 0.6 + - - -
39C VAL* 1.4 75.9 - - - +
41C LYS* 1.4 66.9 + - - +
42C ALA* 3.9 12.3 + - - +
43C THR* 3.1 23.2 + - - -
44C PHE* 2.9 21.3 + - - +
34D GLU* 5.5 5.7 - - - +
35D PRO 4.5 3.7 + - - -
36D ALA* 4.4 2.9 - - - +
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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