Contacts of the strand formed by residues 33 - 38 (chain F) in PDB entry 5U07
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 LYS 33 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168B ASN* 4.7 18.2 - - - +
28F VAL 3.5 0.2 - - - +
29F VAL* 4.2 1.3 - - - -
30F TYR 3.0 30.4 + - - +
31F GLY 3.2 2.1 - - - +
32F GLY* 1.3 79.9 - - - +
34F GLU* 1.3 72.9 + - - +
35F ARG* 3.4 5.7 + - - +
196F GLY* 3.4 25.7 - - - +
303F ALA* 3.5 29.4 - - + +
304F LEU 4.3 5.3 + - - -
305F TYR* 4.2 24.2 + - - +
307G SER* 3.7 23.5 + - - +
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Residues in contact with GLU 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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168B ASN* 5.7 6.6 + - + +
27F THR* 3.0 38.7 - - - +
28F VAL 3.5 6.5 - - - +
29F VAL* 4.1 11.6 - - + +
32F GLY 4.3 0.6 + - - -
33F LYS* 1.3 73.4 - - - +
35F ARG* 1.3 59.7 + - - +
36F THR* 4.3 1.7 - - - +
196F GLY* 3.4 7.6 - - - -
197F THR 2.7 42.3 + - - +
198F THR* 4.2 7.1 - - - +
199F VAL* 4.9 7.6 + - - +
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Residues in contact with ARG 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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27F THR* 4.4 2.5 - - - -
28F VAL* 2.8 45.3 + - + +
30F TYR* 3.2 37.3 + - + -
31F GLY* 4.7 0.2 - - - -
33F LYS* 3.7 6.0 + - - +
34F GLU* 1.3 75.0 - - - +
36F THR* 1.3 64.3 + - - +
192F PHE* 3.5 23.6 - - + -
193F THR* 3.0 31.3 + - - +
194F VAL 3.1 20.0 + - - -
195F HIS 3.9 6.5 - - - +
196F GLY* 4.3 1.1 - - - -
197F THR 4.3 3.8 - - - +
300F PHE 2.8 22.8 + - - -
301F GLU 3.6 5.3 + - - -
303F ALA* 3.1 37.2 - - - +
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Residues in contact with THR 36 (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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25F PRO* 4.3 13.9 - - + -
26F LYS 3.4 8.7 - - - -
27F THR* 4.0 17.5 - - + +
34F GLU* 4.3 0.9 - - - +
35F ARG* 1.3 71.2 - - - +
37F ARG* 1.3 59.3 + - - +
192F PHE* 3.6 0.3 - - - -
193F THR* 3.0 39.6 + - - +
197F THR* 3.0 32.1 + - - +
199F VAL* 5.4 2.7 - - + +
227F SER* 3.5 26.3 + - - +
228F ALA 4.8 0.9 + - - -
231F PHE* 3.9 10.5 - - - -
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Residues in contact with ARG 37 (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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18F ASN* 3.8 5.0 - - - +
25F PRO* 5.4 1.4 - - - +
26F LYS* 2.7 62.5 + - - +
27F THR 4.2 6.3 + - - +
28F VAL* 3.3 30.5 - - + +
36F THR* 1.3 75.6 - - - +
38F VAL* 1.3 63.9 + - - +
39F SER* 3.6 17.6 - - - +
190F HIS* 3.7 13.9 + - + -
191F ALA 3.2 13.5 - - - +
192F PHE* 4.1 6.1 - - + -
231F PHE* 5.1 1.6 - - - -
14G TYR* 2.8 36.0 + - - -
200G GLU* 4.8 3.8 + - - -
201G VAL 4.6 3.4 + - - -
202G ASP* 2.4 40.6 + - - +
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Residues in contact with VAL 38 (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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17F ILE* 3.3 40.2 - - + -
18F ASN* 3.3 20.2 - - - +
37F ARG* 1.3 76.0 - - - +
39F SER* 1.3 66.0 + - - +
40F SER* 3.5 0.3 + - - -
42F SER* 3.6 10.8 - - - +
43F TRP* 4.5 10.7 - - + +
188F PHE* 5.8 0.7 - - - -
190F HIS* 3.9 2.9 - - - -
191F ALA* 2.8 37.8 + - + +
231F PHE* 3.3 27.1 - - + -
268F PRO* 4.2 8.3 - - + -
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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