Contacts of the strand formed by residues 45 - 51 (chain A) in PDB entry 2VSC
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 ARG 45 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A LYS* 3.2 5.0 - - - +
42A PHE* 3.0 45.1 + - - +
43A LYS* 3.3 8.7 - - + +
44A GLY* 1.3 77.6 - - - +
46A ASP* 1.3 69.3 + - - +
47A ILE* 3.3 8.1 + - + +
60A PRO* 3.6 19.4 - - - +
62A ASP* 3.1 39.8 + - - -
63A PHE* 4.6 7.5 - - - -
90A HIS* 5.4 1.6 + - - -
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Residues in contact with ASP 46 (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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39A LYS* 3.4 35.4 + - + +
40A TRP 3.5 6.3 - - - -
41A LYS* 3.7 13.0 + - - +
44A GLY 5.6 0.2 - - - -
45A ARG* 1.3 76.0 + - - +
47A ILE* 1.3 62.6 + - - +
48A TYR* 3.4 1.5 - - - -
49A THR* 4.0 20.9 - - + +
58A THR 5.6 0.3 - - - +
60A PRO* 3.9 11.8 - - - +
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Residues in contact with ILE 47 (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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40A TRP* 2.7 23.3 + - + +
41A LYS 4.3 0.7 - - - -
42A PHE* 3.9 28.0 - - + +
45A ARG* 3.6 24.9 - - - +
46A ASP* 1.3 73.5 - - - +
48A TYR* 1.3 64.1 + - + +
59A VAL* 4.0 4.5 - - - +
60A PRO* 3.2 25.4 - - + +
63A PHE* 3.3 54.4 - - + +
66A ALA* 4.1 1.3 - - + +
80A LEU* 3.6 31.4 - - + -
94A TYR* 4.1 5.2 - - + -
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Residues in contact with TYR 48 (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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38A VAL* 4.7 2.5 - - + -
39A LYS* 3.3 2.3 - - - -
40A TRP* 2.7 53.9 + + + +
46A ASP 3.4 1.0 - - - -
47A ILE* 1.3 82.3 - - + +
49A THR* 1.3 78.7 + - - +
50A PHE* 3.6 9.9 - - + +
57A SER* 2.5 38.2 + - - -
58A THR 3.6 6.1 - - - -
59A VAL* 3.4 19.5 - - + -
66A ALA* 3.5 13.7 - - + -
67A LYS* 3.6 16.6 - - + +
68A ILE* 3.3 43.3 + - + +
70A VAL* 5.1 1.4 - - - +
80A LEU* 3.8 17.9 - - + -
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Residues in contact with THR 49 (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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37A TYR* 3.8 23.5 + - + +
38A VAL 3.0 8.1 - - - -
39A LYS* 3.9 22.0 - - + -
46A ASP* 4.0 17.9 - - + +
48A TYR* 1.3 84.8 - - - +
50A PHE* 1.3 60.4 + - - +
51A ASP* 5.1 1.4 + - - +
57A SER* 3.2 8.1 - - - -
58A THR* 3.0 45.9 + - - +
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Residues in contact with PHE 50 (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 THR* 4.3 8.5 - - - -
36A VAL 4.5 2.9 - - - -
37A TYR* 3.5 11.5 - - - -
38A VAL* 2.7 36.2 + - + +
48A TYR* 3.6 18.3 - - + +
49A THR* 1.3 72.0 - - - +
51A ASP* 1.3 57.6 + - - +
52A GLY* 3.3 27.8 - - - -
55A ASN* 3.9 16.4 - - - -
56A LYS 3.6 25.8 - - - -
57A SER* 3.6 14.8 - - - -
68A ILE* 3.9 11.2 - - + -
70A VAL* 3.8 33.9 - - + -
73A LEU* 3.7 31.2 - - + -
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Residues in contact with ASP 51 (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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37A TYR* 3.6 30.5 + - + +
49A THR* 4.1 1.9 + - - +
50A PHE* 1.3 70.3 - - - +
52A GLY* 1.3 60.4 + - - +
53A ALA* 3.3 20.4 + - - +
54A LEU* 3.0 36.1 + - + +
55A ASN 2.8 23.0 + - - -
56A LYS* 3.0 18.7 + - + +
101A LEU* 5.9 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