Contacts of the strand formed by residues 28 - 33 (chain A) in PDB entry 2VXO
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 28 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A ALA* 1.3 81.1 - - - +
29A VAL* 1.3 71.5 + - - +
30A ILE* 4.9 0.2 - - + -
45A VAL* 5.0 0.9 - - + -
50A VAL* 4.3 2.7 - - + -
51A GLN 2.9 10.3 + - - +
52A SER* 3.3 12.7 + - - +
53A GLU 3.2 22.5 + - - -
69A PHE* 3.8 3.8 - - - -
71A ALA* 3.5 28.3 - - + +
73A ILE* 3.8 30.1 - - + -
207A LEU* 3.8 24.0 - - + -
213A CYS* 3.9 17.7 - - - -
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Residues in contact with VAL 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A VAL* 1.3 74.3 - - - +
30A ILE* 1.3 62.3 + - - +
31A LEU* 3.9 8.3 - - + -
53A GLU 3.4 10.5 - - - +
55A PHE* 3.8 38.4 - - + -
64A ILE* 3.9 22.7 - - + -
69A PHE* 3.7 18.5 - - + -
71A ALA 3.1 12.9 + - - +
72A ILE* 3.4 23.4 - - + +
73A ILE 2.8 31.9 + - - +
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Residues in contact with ILE 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A VAL* 4.9 0.4 - - + -
29A VAL* 1.3 76.1 - - - +
31A LEU* 1.3 71.7 + - - +
38A GLY* 4.0 24.2 - - - +
41A ILE* 3.8 30.1 - - + -
42A ASP* 3.6 37.9 - - + +
52A SER* 3.0 28.5 - - - +
53A GLU 2.9 11.2 + - - +
54A ILE* 3.4 12.3 - - + +
55A PHE 2.9 29.6 + - - +
73A ILE* 3.3 15.0 - - + +
75A SER* 4.9 0.2 - - - +
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Residues in contact with LEU 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A VAL* 3.9 9.0 - - + -
30A ILE* 1.3 76.0 - - - +
32A ASP* 1.3 59.7 + - - +
55A PHE* 3.6 25.4 - - + +
56A PRO 3.5 21.5 - - - +
57A LEU* 4.5 21.3 - - + +
59A THR* 4.2 9.4 - - - +
64A ILE* 4.4 6.1 - - + -
72A ILE* 4.0 21.3 - - + -
73A ILE 2.7 11.8 + - - +
74A ILE* 3.3 10.4 - - + +
75A SER 3.0 24.8 + - - +
93A ILE* 3.8 38.1 - - + -
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Residues in contact with ASP 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A ILE* 4.0 3.2 + - + -
31A LEU* 1.3 74.3 - - - +
33A ALA* 1.3 72.2 + - - +
34A GLY* 2.7 27.2 + - - +
37A TYR* 3.2 13.3 + - - +
38A GLY* 2.4 41.2 + - - +
54A ILE* 4.8 7.4 - - + +
55A PHE 4.1 6.2 + - - +
57A LEU* 3.9 8.8 + - - +
75A SER* 3.4 17.0 + - - +
76A GLY* 3.9 4.2 - - - -
541B GLU* 2.7 28.8 - - - +
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Residues in contact with ALA 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A ASP* 1.3 77.2 + - - +
34A GLY* 1.3 55.5 + - - +
57A LEU* 4.3 19.1 - - + -
75A SER 2.9 14.5 + - - +
76A GLY* 3.8 11.0 - - - -
77A GLY 3.9 4.9 + - - -
87A PRO* 5.0 5.6 - - + -
105A TYR* 4.2 24.6 - - + -
109A MET* 4.5 2.2 - - + -
541B GLU* 3.0 11.4 - - - +
655B ASN* 3.8 12.4 + - - +
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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