Contacts of the strand formed by residues 40 - 45 (chain D) in PDB entry 4UX9
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 VAL 40 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31D PRO* 3.7 4.5 - - - +
32D ILE* 3.0 46.9 + - + +
39D ILE* 1.4 81.1 - - - +
41D CYS* 1.3 69.0 + - - +
53D ALA* 4.1 6.7 - - + -
54D ILE 3.2 14.8 - - - +
55D LYS* 3.9 21.8 - - + +
108D MET* 5.3 0.9 - - + -
168D LEU* 5.9 0.7 - - + -
1000D ANP 3.7 62.0 + - + +
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Residues in contact with CYS 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D ILE* 3.6 40.8 - - - -
20D PHE* 3.9 17.7 - - + -
29D LEU* 4.0 28.7 - - + -
30D LYS 3.3 7.2 - - - +
31D PRO* 4.0 15.9 - - - -
32D ILE* 4.1 5.8 - - - -
40D VAL* 1.3 73.3 - - - +
42D ALA* 1.3 59.9 + - - +
53D ALA* 3.3 4.7 - - - -
54D ILE* 2.8 34.9 + - + +
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Residues in contact with ALA 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28D ASN 3.6 2.7 - - - +
29D LEU* 3.3 5.5 - - - -
30D LYS* 2.8 37.5 + - + +
32D ILE* 3.8 21.8 - - + +
41D CYS* 1.3 72.8 - - - +
43D ALA* 1.3 58.5 - - - +
52D VAL 3.4 6.1 - - - +
110D LEU* 4.0 24.5 - - + -
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Residues in contact with ALA 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26D TYR* 4.2 7.2 - - + -
27D GLN 3.5 11.9 - - - +
28D ASN 4.4 1.1 - - - -
29D LEU* 3.8 14.1 - - + -
41D CYS 4.0 0.4 + - - +
42D ALA* 1.3 75.6 - - - +
44D TYR* 1.3 59.9 - - - +
45D ASP 3.8 0.2 - - - -
51D ASN* 3.4 6.4 - - - +
52D VAL* 2.7 42.9 + - + +
54D ILE* 3.8 28.5 - - + -
110D LEU* 5.5 0.2 - - - +
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Residues in contact with TYR 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D ARG 3.2 4.3 - - - +
26D TYR* 4.5 0.9 - - - -
27D GLN* 2.9 59.0 + - + +
28D ASN* 4.9 3.8 + - + -
43D ALA* 1.3 72.5 - - - +
45D ASP* 1.4 57.0 + - - +
46D ALA* 3.4 19.8 + - + -
49D GLU* 3.2 49.5 + - - +
50D ARG* 3.6 9.6 - - - -
51D ASN* 3.5 21.8 - - - +
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Residues in contact with ASP 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D ARG* 2.8 45.8 + - - +
26D TYR* 3.3 21.7 + - + -
43D ALA 3.7 2.4 + - - -
44D TYR* 1.4 69.2 - - - +
46D ALA* 1.3 57.8 + - - +
47D ILE 3.0 15.9 + - - -
48D LEU* 3.2 23.2 + - + +
49D GLU* 2.9 25.3 + - - -
50D ARG 2.8 23.1 + - - +
52D VAL* 3.8 15.9 - - + +
107D VAL* 5.3 0.7 - - - +
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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