Contacts of the strand formed by residues 29 - 35 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23F PHE* 4.2 1.8 - - - -
24F ASN* 3.0 28.5 + - + +
27F THR* 2.9 32.1 + - - +
28F GLY* 1.3 80.3 - - - +
30F ILE* 1.3 65.7 + - - +
31F GLY* 3.2 0.9 + - - -
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Residues in contact with ILE 30 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1F MET* 4.0 22.0 - - - +
21F ASN* 3.7 35.2 - - + +
22F VAL 3.9 4.7 - - - +
23F PHE* 3.8 22.7 - - + -
28F GLY 4.0 0.8 + - - -
29F GLU* 1.3 73.7 - - - +
31F GLY* 1.3 62.4 + - - +
32F LYS 3.7 18.8 - - - +
33F GLN* 4.2 4.5 - - - +
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Residues in contact with GLY 31 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1F MET* 3.6 23.0 - - - +
22F VAL* 3.1 10.3 + - - -
23F PHE* 4.5 0.6 - - - +
24F ASN* 5.3 5.4 - - - -
29F GLU 3.2 6.1 + - - -
30F ILE* 1.3 74.5 - - - +
32F LYS* 1.3 70.9 + - - +
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Residues in contact with LYS 32 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1F MET* 4.2 7.6 - - - +
2F THR* 3.7 28.0 + - - +
4F ILE* 3.8 28.8 - - + +
21F ASN* 3.8 1.6 - - - -
22F VAL* 3.1 37.2 + - + +
30F ILE* 3.7 9.2 - - - +
31F GLY* 1.3 84.4 - - - +
33F GLN* 1.3 63.4 + - - +
88F GLU* 5.3 16.1 + - - +
89F GLU* 4.1 7.4 - - + +
179F SER* 3.6 20.8 + - - +
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Residues in contact with GLN 33 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1F MET* 3.9 31.6 - - + +
2F THR 3.4 7.8 + - - +
3F THR* 3.3 18.9 - - + +
4F ILE* 2.7 35.6 + - - +
19F SER* 2.6 32.7 + - - +
20F GLN* 3.5 13.5 + - - +
21F ASN* 2.6 27.6 + - - +
22F VAL* 4.6 1.1 - - - -
30F ILE* 4.2 3.4 - - - +
32F LYS* 1.3 80.5 + - - +
34F LEU* 1.3 54.4 + - - +
35F ASP 4.0 0.2 - - - -
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Residues in contact with LEU 34 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3F THR* 4.6 0.2 - - - -
4F ILE* 3.7 19.3 - - + +
19F SER* 3.3 5.1 - - - -
20F GLN* 2.8 36.5 + - + +
22F VAL* 3.6 17.4 - - + +
33F GLN* 1.3 70.2 - - - +
35F ASP* 1.3 70.7 + - - +
36F LEU* 3.6 12.7 + - + +
175F GLU* 3.4 47.1 - - + +
178F PRO* 3.7 16.6 - - + -
202F ASN* 3.5 36.1 - - + +
203F GLY 4.7 0.4 - - - +
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Residues in contact with ASP 35 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3F THR* 4.0 10.7 - - + +
4F ILE 3.1 18.8 + - - +
5F GLY* 4.7 0.9 - - - -
6F HIS* 3.0 30.9 + - + +
14F THR* 3.3 18.7 + - - +
15F GLU* 2.7 32.8 + - - +
16F ASN* 3.2 18.6 + - - +
17F THR 4.2 0.5 + - - -
18F ARG 3.2 17.7 - - - +
19F SER* 4.5 2.9 - - - +
34F LEU* 1.3 86.6 - - - +
36F LEU* 1.3 61.0 + - - +
37F ALA 4.0 0.4 - - - -
202F ASN 3.8 3.1 - - - +
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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