Contacts of the strand formed by residues 53 - 57 (chain A) in PDB entry 2VUT
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 53 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A ILE* 4.0 25.4 - - + -
26A ALA* 3.9 11.2 - - + -
32A VAL* 3.6 14.1 - - + -
34A ALA* 5.3 0.7 - - + -
47A LEU* 3.6 18.2 - - + +
48A GLN* 4.8 4.0 + - - +
50A ILE* 3.3 43.1 - - + +
51A PRO 2.8 12.1 + - - +
52A ASN* 1.3 78.0 - - - +
54A THR* 1.3 61.4 + - - +
55A LEU* 3.7 26.3 + - + +
51C PRO* 4.7 10.8 - - - +
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Residues in contact with THR 54 (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 VAL 2.8 12.1 + - - +
33A ARG* 3.4 13.0 + - - +
34A ALA* 3.0 25.6 + - - +
52A ASN 3.9 2.1 - - - -
53A VAL* 1.3 73.1 + - - +
55A LEU* 1.3 67.7 + - - +
56A PHE* 3.6 30.8 - - + -
31C HIS* 5.6 1.9 - - - -
51C PRO* 4.8 9.6 - - + +
52C ASN* 3.4 34.0 + - - +
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Residues in contact with LEU 55 (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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13A ALA* 4.5 3.4 - - + -
34A ALA* 3.4 14.4 - - + +
36A VAL* 3.7 28.9 - - + -
39A LEU* 4.1 24.0 - - + -
44A ALA* 4.3 7.0 - - - +
47A LEU* 4.4 6.3 - - + -
48A GLN* 3.7 45.8 - - + +
53A VAL* 3.7 24.1 + - + +
54A THR* 1.3 80.5 - - - +
56A PHE* 1.3 69.4 + - - +
57A GLN 4.1 0.8 + - - -
26C ALA 5.6 1.2 - - - +
27C ALA* 4.8 4.5 - - - +
51C PRO* 5.3 4.4 - - + +
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Residues in contact with PHE 56 (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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33A ARG* 3.5 44.4 - - + -
34A ALA 2.8 15.4 + - - +
35A GLN* 3.2 8.8 - - + +
36A VAL* 3.1 23.3 + - - +
54A THR* 3.6 30.3 - - + -
55A LEU* 1.3 75.5 - - - +
57A GLN* 1.3 62.4 + - - +
58A GLY 3.7 0.7 + - - -
66A LEU* 3.6 22.8 - - + +
69A THR* 3.4 17.9 - - + -
70A LEU* 4.2 16.6 - - + -
26C ALA 5.1 0.9 - - - -
27C ALA 3.9 13.9 - - - -
28C VAL 4.0 2.5 - - - -
29C GLY* 3.3 30.7 - - - -
706K VAL* 4.2 7.0 - - + -
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Residues in contact with GLN 57 (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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36A VAL* 3.3 9.9 - - + +
37A HIS 3.6 13.7 + - - +
38A SER* 3.4 8.7 - - - +
39A LEU* 2.9 60.7 - - + +
40A LYS* 6.0 0.8 - - - +
55A LEU 4.1 1.4 - - - -
56A PHE* 1.3 72.3 - - - +
58A GLY* 1.3 61.3 + - - +
66A LEU* 5.0 0.4 - - - -
27C ALA 5.5 0.4 + - - -
675K ASN* 6.1 0.2 - - - -
706K VAL* 3.0 14.7 - - + +
707K VAL* 2.9 56.3 + - + +
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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