Contacts of the helix formed by residues 41 - 50 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39F LEU 3.4 1.2 + - - -
40F LYS* 1.3 75.8 - - - +
42F LEU* 1.3 67.9 + - - +
43F ILE 3.4 2.2 - - - -
44F ALA* 3.4 5.1 + - - -
45F GLU* 3.1 33.3 + - - +
1353F NAP 5.4 4.0 - - - -
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Residues in contact with LEU 42 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41F GLY* 1.3 73.5 - - - +
43F ILE* 1.3 71.0 + - + +
45F GLU* 3.2 10.7 + - - +
46F GLU* 2.9 21.8 + - - +
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Residues in contact with ILE 43 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14F THR* 3.5 45.1 - - + +
19F ALA* 4.3 6.7 - - + -
23F ARG* 4.1 16.6 - - - +
42F LEU* 1.3 76.7 - - + +
44F ALA* 1.3 67.6 + - - +
46F GLU* 2.9 25.5 + - + +
47F LEU* 2.8 41.8 + - + +
193F GLU* 5.2 3.4 - - - +
1353F NAP 5.6 3.8 - - - +
711N SER* 6.2 0.9 - - - -
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Residues in contact with ALA 44 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14F THR* 3.6 18.6 - - + +
36F VAL* 5.5 1.3 - - + -
38F SER 3.7 13.5 - - - +
39F LEU* 3.3 35.9 - - + +
40F LYS 4.2 3.1 - - - +
41F GLY* 3.4 8.2 + - - +
42F LEU 3.3 0.2 - - - -
43F ILE* 1.3 79.1 - - - +
45F GLU* 1.3 57.3 + - - +
47F LEU* 3.3 4.3 + - - +
48F GLN* 2.8 30.1 + - - +
55F LEU* 4.1 6.1 - - - +
1353F NAP 5.0 1.5 + - - +
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Residues in contact with GLU 45 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39F LEU 4.0 11.6 - - - +
40F LYS* 5.3 1.4 - - - -
41F GLY 3.1 26.2 + - - +
42F LEU* 3.5 10.4 - - - +
44F ALA* 1.3 74.6 - - - +
46F GLU* 1.3 63.1 + - - +
48F GLN* 3.0 11.9 - - - +
49F ALA* 2.9 22.0 + - - +
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Residues in contact with GLU 46 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23F ARG* 2.6 40.0 + - - +
42F LEU 2.9 12.1 + - - +
43F ILE* 2.9 31.3 + - - +
45F GLU* 1.3 76.4 - - - +
47F LEU* 1.3 66.9 + - + +
49F ALA* 2.9 22.4 + - - +
50F ILE* 3.2 15.1 + - + +
710N LEU 4.6 0.3 - - - +
711N SER* 4.3 3.9 - - - -
712N LEU* 3.8 31.3 + - - +
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Residues in contact with LEU 47 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13F ALA* 3.4 42.6 - - + +
14F THR* 3.8 16.2 - - + -
19F ALA* 4.3 16.8 - - + +
22F ILE* 4.4 17.0 - - + -
23F ARG* 4.9 0.4 - - + -
36F VAL* 4.6 3.8 - - + -
43F ILE* 2.8 28.6 + - + +
44F ALA* 3.7 3.1 - - - +
46F GLU* 1.3 77.9 - - - +
48F GLN* 1.3 69.9 + - - +
49F ALA 3.2 0.3 + - - -
50F ILE* 3.2 37.4 + - + +
53F VAL* 3.8 16.8 - - + +
55F LEU* 4.3 9.9 - - + -
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Residues in contact with GLN 48 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39F LEU* 4.0 23.6 - - + +
44F ALA 2.8 15.5 + - - +
45F GLU* 3.0 19.3 - - - +
47F LEU* 1.3 78.9 - - - +
49F ALA* 1.3 60.2 + - - +
50F ILE 3.6 5.4 - - - +
53F VAL 4.8 7.9 + - - +
55F LEU* 3.7 23.8 - - + +
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Residues in contact with ALA 49 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45F GLU 2.9 11.7 + - - +
46F GLU* 2.9 13.2 + - - +
48F GLN* 1.3 76.7 - - - +
50F ILE* 1.3 68.3 + - + +
51F PRO* 3.0 9.5 - - - +
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Residues in contact with ILE 50 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22F ILE* 4.7 4.7 - - + -
23F ARG* 4.2 34.1 - - + +
26F ALA* 3.4 31.4 - - + -
27F ALA 5.4 0.4 - - - +
46F GLU* 3.2 15.5 + - + +
47F LEU* 3.2 30.1 + - + +
48F GLN 3.6 7.6 - - - +
49F ALA* 1.3 75.9 - - + +
51F PRO* 1.4 75.9 - - + +
52F ASN 4.6 1.1 - - - +
53F VAL* 3.5 18.7 + - + +
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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