Contacts of the helix formed by residues 41 - 50 (chain E) in PDB entry 2VUU
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 GLY 41 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39E LEU 3.6 1.6 + - - -
40E LYS* 1.3 74.4 - - - +
42E LEU* 1.3 66.4 + - - -
43E ILE 3.4 2.2 - - - -
44E ALA* 3.4 5.1 + - - -
45E GLU* 3.0 34.5 + - - +
1353E NAP 5.3 3.8 - - - -
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Residues in contact with LEU 42 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41E GLY* 1.3 72.0 - - - +
43E ILE* 1.3 82.9 + - + +
45E GLU* 3.3 6.8 + - - +
46E GLU* 2.9 34.9 + - + +
711M LEU* 5.0 26.5 - - + +
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Residues in contact with ILE 43 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14E THR* 3.7 42.6 - - + +
19E ALA* 4.3 11.7 - - + -
23E ARG* 3.8 11.0 - - - +
41E GLY 3.4 0.2 - - - -
42E LEU* 1.3 94.2 - - + +
44E ALA* 1.3 67.7 + - - +
46E GLU* 3.0 16.8 + - - +
47E LEU* 2.9 40.7 + - + +
193E GLU* 5.5 5.2 - - - +
1353E NAP 5.6 4.5 - - - +
711M LEU 5.9 0.4 - - - +
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Residues in contact with ALA 44 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14E THR* 3.6 17.7 - - + +
36E VAL* 5.6 1.6 - - + -
38E SER 3.6 20.6 - - - +
39E LEU* 3.6 27.8 - - + +
40E LYS 4.3 1.3 - - - +
41E GLY* 3.4 10.2 + - - +
42E LEU 3.3 0.2 - - - -
43E ILE* 1.3 79.2 - - - +
45E GLU* 1.3 57.4 + - - +
47E LEU* 3.4 4.7 + - - +
48E GLN* 2.8 31.4 + - - +
55E LEU* 4.0 5.7 - - - +
1353E NAP 5.2 1.1 + - - +
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Residues in contact with GLU 45 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39E LEU 3.9 12.9 - - - +
40E LYS* 5.1 1.4 - - - -
41E GLY 3.0 25.8 + - - +
42E LEU* 3.6 5.6 - - - +
44E ALA* 1.3 73.5 - - - +
46E GLU* 1.3 67.2 + - - +
48E GLN* 3.1 16.3 + - - +
49E ALA* 3.0 20.6 + - - +
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Residues in contact with GLU 46 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23E ARG* 2.6 52.0 + - - +
42E LEU* 2.9 19.7 + - + +
43E ILE* 3.1 21.7 - - - +
45E GLU* 1.3 75.2 - - - +
47E LEU* 1.3 62.4 + - + +
49E ALA* 2.8 29.0 + - - +
50E ILE* 3.2 17.1 + - + +
709M LEU 4.4 1.9 - - - +
710M SER* 3.7 7.6 - - - -
711M LEU* 3.8 24.1 + - - +
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Residues in contact with LEU 47 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13E ALA* 3.5 39.9 - - + +
14E THR* 4.0 7.6 - - + -
19E ALA* 4.4 14.8 - - + +
22E ILE* 3.6 28.3 - - + -
23E ARG* 4.9 3.6 - - + -
36E VAL* 5.3 0.9 - - + -
43E ILE* 2.9 35.5 + - + +
44E ALA* 3.8 3.8 - - - +
46E GLU* 1.3 78.9 - - + +
48E GLN* 1.3 63.3 + - - +
49E ALA 3.2 0.7 + - - -
50E ILE* 3.3 29.8 + - + +
53E VAL* 3.7 18.8 - - + +
55E LEU* 4.4 14.8 - - + -
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Residues in contact with GLN 48 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39E LEU* 3.6 42.4 - - - +
44E ALA 2.8 16.6 + - - +
45E GLU* 3.3 18.3 - - - +
47E LEU* 1.3 78.5 - - - +
49E ALA* 1.3 61.6 + - - +
50E ILE 3.8 4.5 - - - +
53E VAL* 4.8 5.2 - - - +
55E LEU* 3.8 16.6 - - + +
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Residues in contact with ALA 49 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45E GLU 3.0 9.5 + - - +
46E GLU* 2.8 16.3 + - - +
48E GLN* 1.3 75.5 - - - +
50E ILE* 1.3 66.0 + - + +
51E PRO* 3.1 9.2 - - - +
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Residues in contact with ILE 50 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22E ILE* 4.4 11.0 - - + -
23E ARG* 4.5 17.0 - - + +
26E ALA* 3.5 30.1 - - + -
27E ALA 5.4 0.2 - - - +
46E GLU* 3.2 17.2 + - + +
47E LEU* 3.3 42.4 + - + +
48E GLN 3.8 4.7 - - - +
49E ALA* 1.3 77.6 - - + +
51E PRO* 1.3 78.6 - - + +
52E ASN 3.8 1.3 - - - +
53E VAL* 3.7 15.8 + - + +
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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