Contacts of the helix formed by residues 38 - 48 (chain W) in PDB entry 1VQN
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 THR 38 (chain W).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10230 C 6.2 0.2 - - - +
36W PRO* 3.2 19.1 + - - +
37W GLU* 1.3 77.3 + - - +
39W ASP* 1.3 74.5 + - + +
40W ALA* 3.3 16.2 - - + +
41W TYR* 4.2 15.1 - - + +
42W ARG* 2.8 29.7 + - - +
103W GLU* 5.3 0.9 + - - -
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Residues in contact with ASP 39 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9460 C 3.4 34.8 + - - +
9470 U 5.6 3.0 - - - +
38W THR* 1.3 79.4 - - + +
40W ALA* 1.3 66.9 + - - +
42W ARG* 2.7 53.1 + - - +
43W GLY 3.1 11.3 + - - -
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Residues in contact with ALA 40 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9450 U 2.6 36.5 + - - +
9460 C 3.4 18.5 + - - +
10220 A 4.7 7.0 - - + +
10230 C 4.3 22.2 - - - +
38W THR* 3.3 11.1 - - + +
39W ASP* 1.3 79.0 - - - +
41W TYR* 1.3 62.4 + - + +
43W GLY 3.4 0.9 + - - -
44W MET* 3.5 13.5 + - + +
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Residues in contact with TYR 41 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10230 C 3.5 19.5 - - - -
10240 G 3.0 35.9 + - - -
24W LEU* 3.7 23.8 - - + -
35W VAL* 3.3 25.6 - - + -
36W PRO* 3.3 47.0 - - + +
38W THR* 3.5 19.7 + - + +
39W ASP 3.3 0.4 - - - -
40W ALA* 1.3 79.1 - - + +
42W ARG* 1.3 61.4 + - - +
44W MET* 3.2 21.7 + - + +
45W VAL* 3.1 26.7 + - - +
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Residues in contact with ARG 42 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9460 C 4.9 10.3 + - - -
9470 U 5.1 4.4 + - - -
31019 G 5.6 4.6 + - - -
37W GLU* 6.3 0.7 - - - +
38W THR 2.8 18.6 + - - +
39W ASP* 2.7 45.1 + - - +
41W TYR* 1.3 77.6 - - - +
43W GLY* 1.3 61.5 + - - +
45W VAL* 3.0 26.8 - - + +
46W ALA* 3.1 11.6 + - + +
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Residues in contact with GLY 43 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9450 U 3.1 31.3 - - - +
9460 C 4.3 7.4 - - - -
39W ASP 3.1 11.3 + - - -
40W ALA 3.4 0.6 + - - -
41W TYR 3.3 0.2 - - - -
42W ARG* 1.3 75.9 - - - +
44W MET* 1.3 62.3 + - - +
46W ALA* 3.3 7.9 + - - +
47W LYS* 3.0 22.9 + - - +
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Residues in contact with MET 44 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9440 G 3.1 41.1 - - - +
9450 U 3.5 20.4 + - - +
10230 C 4.3 4.3 - - - +
10240 G 4.7 9.0 - - - +
20W THR* 4.0 15.7 - - + -
23W MET* 5.1 4.7 - - - -
24W LEU* 4.0 25.4 - - + -
40W ALA* 3.5 15.6 + - + +
41W TYR* 3.2 43.2 + - + +
43W GLY* 1.3 75.5 - - - +
45W VAL* 1.3 63.1 + - - +
47W LYS* 3.0 15.0 + - - +
48W VAL* 3.2 17.1 + - - +
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Residues in contact with VAL 45 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2W HIS* 5.7 7.4 - - + +
4W LEU* 3.6 38.4 - - + -
24W LEU* 4.7 3.1 - - + -
35W VAL* 4.5 14.6 - - + -
41W TYR 3.1 11.4 + - - +
42W ARG* 3.0 25.6 - - + +
44W MET* 1.3 75.1 - - - +
46W ALA* 1.3 58.2 + - + +
48W VAL* 3.1 7.1 + - - +
49W ASN* 2.8 29.5 + - - +
52W VAL* 5.0 1.2 - - - +
54W PHE* 4.8 26.8 - - + -
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Residues in contact with ALA 46 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30839 G 5.2 7.7 + - - -
30999 U 4.5 3.1 + - - -
31009 G 4.5 27.0 - - - +
42W ARG* 3.1 15.8 + - + +
43W GLY* 3.5 8.3 - - - +
45W VAL* 1.3 83.6 - - + +
47W LYS* 1.3 59.1 + - - +
49W ASN* 3.0 29.2 - - - +
50W ASP* 5.2 1.0 - - - +
54W PHE* 6.1 0.9 - - - -
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Residues in contact with LYS 47 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9440 G 3.3 24.9 + - - +
9450 U 3.2 20.8 + - - +
30839 G 6.3 0.7 - - - +
30849 G 4.7 6.4 + - - -
16W ASP* 3.0 49.6 + - - -
17W ILE* 4.1 26.4 - - + +
20W THR* 3.4 15.7 - - - +
43W GLY 3.0 13.9 + - - +
44W MET* 3.0 11.0 + - - +
46W ALA* 1.3 78.0 - - - +
48W VAL* 1.3 58.4 + - + +
49W ASN 3.2 1.2 + - - -
50W ASP* 4.8 2.3 - - - +
51W PHE* 5.3 0.5 - - - -
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Residues in contact with VAL 48 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4W LEU* 5.6 1.6 - - + -
17W ILE* 4.0 14.6 - - + +
20W THR* 3.5 36.1 - - + -
21W LEU* 3.1 42.2 - - + -
24W LEU* 4.9 3.1 - - + -
44W MET 3.2 6.0 + - - +
45W VAL* 3.1 8.7 + - - +
47W LYS* 1.3 76.4 - - - +
49W ASN* 1.3 63.9 + - - +
50W ASP 2.9 4.9 + - - -
51W PHE* 3.0 19.3 + - + -
52W VAL* 3.4 21.1 - - + +
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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