Contacts of the strand formed by residues 39 - 47 (chain A) in PDB entry 1VQ4
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 ALA 39 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A VAL 4.1 2.2 - - - +
38A ILE* 1.3 76.5 - - - +
40A GLY* 1.3 57.8 + - - +
60A PHE* 3.3 13.7 - - - -
61A GLU* 2.9 50.0 + - - +
79A GLU* 4.1 18.6 - - - +
80A LEU 3.4 13.9 - - - +
81A GLN* 4.2 10.8 - - + +
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Residues in contact with GLY 40 (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 ALA* 1.3 77.7 - - - +
41A THR* 1.3 62.6 + - - -
58A VAL* 4.1 8.1 - - - -
59A GLU 3.0 14.8 - - - -
60A PHE* 3.7 10.0 - - - -
61A GLU* 4.5 2.2 - - - -
79A GLU* 3.3 7.6 - - - +
80A LEU* 2.9 33.0 + - - +
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Residues in contact with THR 41 (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 GLY* 1.3 75.8 + - - -
42A VAL* 1.3 76.4 + - - +
43A VAL* 3.2 8.3 + - + +
58A VAL* 3.5 3.1 - - - +
59A GLU* 2.8 35.5 + - - -
77A GLY* 3.4 18.8 + - - +
78A ASP 3.4 12.9 + - - +
79A GLU* 4.5 10.7 + - - +
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Residues in contact with VAL 42 (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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41A THR* 1.3 75.5 - - - +
43A VAL* 1.3 60.3 + - - +
44A ASP 3.9 13.9 - - - +
45A ILE* 4.0 10.8 - - + -
56A ALA* 4.5 2.7 - - + -
57A ALA 3.4 11.4 - - - +
58A VAL* 4.2 4.7 - - + -
74A VAL* 3.6 24.7 - - + -
75A GLY 3.3 26.9 - - - +
76A VAL* 3.4 12.2 - - - +
77A GLY* 3.0 20.1 + - - -
78A ASP* 2.9 19.3 + - + +
80A LEU* 4.0 22.4 - - + -
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Residues in contact with VAL 43 (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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41A THR* 3.2 13.4 + - + +
42A VAL* 1.3 74.1 - - - +
44A ASP* 1.3 61.8 + - + +
57A ALA 2.7 16.3 + - - +
59A GLU* 3.3 45.8 - - + +
65A ARG* 3.9 23.6 - - - +
76A VAL* 3.6 13.7 - - - +
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Residues in contact with ASP 44 (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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42A VAL* 3.6 3.3 - - - +
43A VAL* 1.3 86.0 - - + +
45A ILE* 1.3 84.0 + - - +
46A GLU* 3.8 15.5 - - - +
57A ALA* 2.8 37.7 + - + +
65A ARG* 5.2 2.9 - - - +
76A VAL* 3.9 9.0 - - - +
63Z LYS* 2.8 34.8 + - - +
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Residues in contact with ILE 45 (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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42A VAL* 4.0 11.4 - - + -
44A ASP* 1.3 94.6 + - - +
46A GLU* 1.3 62.4 + - - +
54A PRO* 4.0 15.5 - - + -
55A VAL 3.6 3.8 - - - +
56A ALA* 3.8 22.2 - - + -
74A VAL* 4.2 7.9 - - + +
76A VAL* 4.3 5.2 - - + -
54Z ILE* 3.5 38.3 - - + +
63Z LYS* 3.8 37.0 + - + +
64Z PHE* 4.3 9.4 - - - -
65Z THR* 4.0 18.6 - - + -
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Residues in contact with GLU 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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24A LYS* 3.5 31.5 + - - +
44A ASP* 3.8 15.6 - - - +
45A ILE* 1.3 78.3 - - - +
47A HIS* 1.3 59.7 + - - +
54A PRO* 3.2 5.4 - - - +
55A VAL* 2.7 46.1 + - + -
57A ALA* 4.1 10.6 - - + +
65A ARG* 4.7 6.9 + - - -
67A LEU* 3.7 28.0 - - + +
54Z ILE* 3.9 5.4 - - - -
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Residues in contact with HIS 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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16530 A 3.3 31.0 + - - -
16540 U 3.2 89.2 + + + +
24A LYS* 2.7 35.6 + - - +
46A GLU* 1.3 73.8 - - - +
48A ASP* 1.3 65.2 + - - +
49A PRO* 3.4 6.2 - - - +
52A SER* 3.9 17.9 - - - -
53A ALA 4.0 5.4 + - - -
54A PRO* 4.5 2.2 - - - -
55A VAL* 4.3 0.8 - - - +
52Z THR* 4.2 14.7 + - - +
54Z ILE* 4.1 9.8 - - + +
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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