Contacts of the strand formed by residues 19 - 24 (chain I) 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 SER 19 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3I THR* 5.5 3.8 - - - -
16I ASN* 6.5 0.2 - - - -
18I ARG* 1.3 80.5 - - - +
20I GLN* 1.3 61.2 + - - +
33I GLN* 3.0 25.7 + - - +
34I LEU 3.3 17.3 - - - -
35I ASP* 4.5 3.1 - - - -
36I LEU* 4.0 7.5 - - - +
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Residues in contact with GLN 20 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19I SER* 1.3 76.6 - - - +
21I ASN* 1.3 75.2 + - + +
22I VAL 3.5 0.3 + - - -
33I GLN* 3.6 6.8 - - - -
34I LEU* 2.8 35.5 + - + +
36I LEU* 3.9 28.6 - - + +
175I GLU* 3.4 37.8 + - - +
176I ARG* 5.2 5.9 - - - +
204I ASP* 5.0 6.1 - - - +
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Residues in contact with ASN 21 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20I GLN* 1.3 89.8 + - + +
22I VAL* 1.3 60.9 + - - +
23I PHE* 3.8 29.3 - - + -
30I ILE* 3.5 32.3 - - + +
32I LYS 3.9 4.3 - - - -
33I GLN* 2.5 32.1 + - - +
175I GLU 5.0 1.4 - - - +
176I ARG* 5.9 0.7 - - - -
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Residues in contact with VAL 22 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4I ILE* 4.7 2.2 - - + -
21I ASN* 1.3 75.5 - - - +
23I PHE* 1.3 64.4 + - - +
30I ILE* 3.6 3.5 - - - -
31I GLY* 2.8 24.4 + - - -
32I LYS* 2.8 48.9 + - + +
33I GLN 4.6 0.4 - - - -
34I LEU* 3.6 31.2 - - + +
89I GLU* 3.8 17.3 - - + +
175I GLU 3.9 13.0 - - - +
176I ARG* 4.2 14.4 - - - +
178I PRO* 4.3 9.4 - - + -
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Residues in contact with PHE 23 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21I ASN* 3.8 29.8 - - + -
22I VAL* 1.3 79.3 - - - +
24I ASN* 1.3 61.4 + - - +
25I PRO* 3.6 9.0 - - + +
28I GLY 3.4 27.4 - - - -
29I GLU 3.7 2.7 - - - -
30I ILE* 3.5 29.2 - - + -
31I GLY* 4.5 2.7 - - - -
88I GLU 3.8 5.2 - - - +
89I GLU* 3.9 16.3 - - - +
176I ARG 4.8 3.7 + - - +
324I ILE 5.3 3.6 - - - +
325I THR* 5.7 8.5 - - + -
362I PHE* 4.0 30.5 - + + -
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Residues in contact with ASN 24 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23I PHE* 1.3 73.7 - - - +
25I PRO* 1.3 61.6 - - - +
26I ALA* 3.1 22.0 + - - +
27I THR* 3.2 25.1 + - - +
28I GLY* 2.8 27.0 + - - -
29I GLU* 3.0 12.6 + - + +
31I GLY* 4.5 4.9 - - - +
87I GLY 4.9 2.8 - - - +
88I GLU* 3.5 29.6 + - + +
91I GLY* 5.8 0.2 - - - -
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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