Contacts of the strand formed by residues 29 - 35 (chain E) in PDB entry 4ZZ7
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 GLU 29 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23E PHE* 3.4 4.3 - - - -
24E ASN* 2.9 28.5 + - + +
27E THR* 3.3 30.5 + - - +
28E GLY* 1.3 81.5 - - - +
30E ILE* 1.3 66.6 + - - +
31E GLY 3.3 0.3 + - - -
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Residues in contact with ILE 30 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1E MET* 3.6 30.5 - - + +
21E ASN* 3.3 48.0 - - + +
22E VAL 3.7 7.9 - - - +
23E PHE* 3.7 23.3 - - + -
29E GLU* 1.3 74.1 - - - +
31E GLY* 1.3 62.9 + - - +
32E LYS 4.0 1.3 - - - +
33E GLN* 4.0 5.4 - - - +
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Residues in contact with GLY 31 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1E MET* 3.7 15.1 - - - +
2E THR* 5.1 1.0 + - - -
22E VAL* 3.0 10.0 + - - -
23E PHE* 4.3 0.8 - - - +
24E ASN* 5.0 7.6 - - - -
29E GLU 3.3 5.5 + - - -
30E ILE* 1.3 74.7 - - - +
32E LYS* 1.3 72.2 + - - +
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Residues in contact with LYS 32 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1E MET* 3.8 10.5 - - - -
2E THR* 3.2 32.9 + - - +
4E ILE* 4.0 19.5 - - + +
21E ASN* 3.8 3.8 - - - -
22E VAL* 2.9 40.2 + - + +
30E ILE* 3.7 1.8 - - - +
31E GLY* 1.3 83.9 - - - +
33E GLN* 1.3 62.2 + - - +
85E LEU* 6.1 2.0 - - - +
88E GLU* 4.5 15.1 + - - +
89E GLU* 3.7 20.0 - - + +
179E SER* 3.4 19.8 + - - +
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Residues in contact with GLN 33 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1E MET* 3.8 18.2 - - + +
2E THR 3.0 12.8 + - - +
3E THR* 3.2 15.4 - - + +
4E ILE* 2.8 34.0 + - - +
19E SER* 2.7 33.2 + - - +
20E GLN* 3.5 11.2 + - - -
21E ASN* 2.4 33.6 + - - +
22E VAL* 4.6 1.6 - - - -
30E ILE* 4.0 10.5 - - - +
32E LYS* 1.3 73.8 - - - +
34E LEU* 1.3 55.5 + - - +
35E ASP 4.0 0.4 - - - -
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Residues in contact with LEU 34 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4E ILE* 3.7 21.8 - - + +
19E SER* 3.3 2.9 - - - -
20E GLN* 2.7 37.1 + - + +
22E VAL* 3.8 12.1 - - + -
32E LYS 4.2 0.2 + - - -
33E GLN* 1.3 71.8 - - - +
35E ASP* 1.3 70.4 + - - +
36E LEU* 3.3 16.6 + - + +
175E GLU* 3.4 46.4 - - + +
178E PRO* 3.6 20.6 - - + -
202E ASN* 3.6 31.9 - - + +
203E GLY 4.5 0.9 - - - +
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Residues in contact with ASP 35 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3E THR* 4.2 9.0 - - + +
4E ILE 3.1 18.1 + - - +
5E GLY* 4.6 1.1 - - - -
6E HIS* 2.8 34.7 + - - +
14E THR* 3.6 12.2 - - - +
15E GLU* 2.6 31.7 + - - +
16E ASN* 2.8 29.4 + - - +
17E THR 4.0 0.7 + - - -
18E ARG 3.3 16.3 + - - +
19E SER* 4.4 4.2 - - - +
33E GLN 4.0 2.0 + - - -
34E LEU* 1.3 82.7 - - - +
36E LEU* 1.3 60.5 + - - +
202E ASN 3.8 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