Contacts of the helix formed by residues 51 - 60 (chain X) 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 ASP 51 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13840 C 3.9 0.2 - - - -
49X ARG* 3.7 18.9 + - - +
50X LEU* 1.3 73.3 - - - +
52X PRO* 1.3 68.1 - - - +
53X SER* 2.5 53.6 + - - +
54X ILE* 2.7 21.3 + - - +
55X ASN 3.8 0.5 + - - -
84X ILE* 5.5 3.4 - - + -
85X VAL 2.7 24.3 + - - +
86X GLU* 4.0 11.7 - - + +
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Residues in contact with PRO 52 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13840 C 3.7 30.7 - - - +
13850 G 4.1 14.8 - - - +
13980 G 4.6 6.5 - - - +
13990 A 6.0 1.3 - - - +
49X ARG* 4.2 11.4 - - - +
50X LEU 3.4 3.7 - - - +
51X ASP* 1.3 94.9 - - - +
53X SER* 1.3 62.5 + - - +
54X ILE 3.1 0.4 - - - -
55X ASN* 3.0 8.8 + - + +
56X GLU* 2.8 42.5 + - + +
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Residues in contact with SER 53 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51X ASP* 2.5 28.8 + - - -
52X PRO* 1.3 72.9 - - - +
54X ILE* 1.3 64.1 + - - -
56X GLU* 3.5 8.3 + - - +
57X ALA* 3.0 27.2 + - - +
86X GLU* 3.5 5.2 - - - +
87X ALA* 2.9 35.9 + - - +
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Residues in contact with ILE 54 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30X MET* 4.2 7.6 - - - -
33X ILE* 3.6 33.9 - - + -
50X LEU* 3.9 22.9 - - + -
51X ASP 2.7 16.3 + - - +
53X SER* 1.3 73.1 + - - +
55X ASN* 1.3 66.8 + - - +
57X ALA* 3.0 16.2 + - - +
58X ALA* 3.0 12.6 + - - +
70X ILE* 4.3 8.7 - - + +
72X VAL* 3.3 28.3 - - + -
85X VAL* 3.7 28.3 - - + +
86X GLU 3.8 17.7 - - - -
87X ALA* 3.9 2.5 - - - +
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Residues in contact with ASN 55 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13830 U 2.6 43.8 + - - +
13840 C 3.3 40.6 + - - +
13990 A 4.1 4.6 + - - -
14000 C 4.0 12.7 + - - -
30X MET* 3.2 12.1 - - + +
50X LEU* 5.8 0.4 - - - +
51X ASP 3.8 0.4 + - - -
52X PRO* 3.0 12.2 + - + +
54X ILE* 1.3 81.8 - - - +
56X GLU* 1.3 64.3 + - - +
58X ALA 3.2 0.5 + - - -
59X TRP* 3.0 46.1 + - - -
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Residues in contact with GLU 56 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13990 A 2.9 27.4 + - - +
14000 C 3.4 42.6 + - - +
52X PRO* 2.8 36.4 + - - +
53X SER* 3.9 6.0 - - - +
55X ASN* 1.3 73.4 - - - +
57X ALA* 1.3 59.2 + - - +
59X TRP 3.8 0.3 - - - -
60X ALA* 3.0 28.1 + - - +
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Residues in contact with ALA 57 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53X SER 3.0 14.0 + - - +
54X ILE* 3.0 11.5 + - - +
56X GLU* 1.3 77.0 - - - +
58X ALA* 1.3 62.1 + - - +
60X ALA* 3.2 21.7 - - - +
61X ARG* 4.7 0.5 + - - -
67X PRO* 4.3 12.3 - - + +
70X ILE* 3.9 19.7 - - + -
87X ALA* 5.2 7.2 - - + -
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Residues in contact with ALA 58 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14X LEU* 5.7 2.0 - - + -
26X ALA* 4.3 1.6 - - - +
29X ALA* 4.6 12.1 - - + -
30X MET* 3.2 34.5 - - + -
33X ILE* 5.1 6.3 - - + -
54X ILE 3.0 8.9 + - - +
57X ALA* 1.3 77.6 - - - +
59X TRP* 1.3 59.1 + - + +
61X ARG 5.1 0.3 + - - -
62X GLY 4.0 5.0 - - - +
65X ASN 4.8 0.7 - - - +
66X THR* 2.9 35.3 + - + +
67X PRO* 4.2 10.1 - - + +
70X ILE* 5.0 3.5 - - + +
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Residues in contact with TRP 59 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13810 A 3.7 14.8 - + - -
13820 G 3.6 33.4 - - - -
13830 U 3.1 29.1 + - - -
14000 C 3.7 20.4 - - - +
14010 G 3.7 33.2 - - - +
26X ALA* 3.3 22.8 - - + +
27X ASP* 3.5 22.2 - - - -
30X MET* 3.4 15.1 - - + +
55X ASN* 3.0 45.3 + - - +
56X GLU 3.8 0.9 - - - +
58X ALA* 1.3 77.1 - - - +
60X ALA* 1.3 56.2 + - - +
61X ARG 3.2 2.9 - - - -
62X GLY* 2.7 32.2 + - - -
63X ARG* 3.7 24.5 - - + -
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Residues in contact with ALA 60 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14000 C 5.5 0.4 - - - -
14010 G 4.7 12.3 + - - +
27430 A 4.9 4.5 + - - -
27440 G 5.5 0.2 - - - +
56X GLU 3.0 13.5 + - - +
57X ALA* 3.2 19.2 + - - +
58X ALA 3.4 0.4 - - - -
59X TRP* 1.3 76.0 - - - +
61X ARG* 1.3 72.3 + - + +
62X GLY 3.6 0.2 + - - -
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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