Contacts of the helix formed by residues 41 - 50 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39B LEU 3.5 0.4 + - - -
40B LYS* 1.3 76.0 - - - +
42B LEU* 1.3 67.5 + - - -
43B ILE 3.4 2.0 - - - -
44B ALA* 3.3 5.3 + - - -
45B GLU* 3.0 33.1 + - - +
1353B NAP 5.2 4.7 - - - -
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Residues in contact with LEU 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B GLY* 1.3 69.5 - - - -
43B ILE* 1.3 74.7 + - + +
45B GLU* 2.8 38.5 - - + +
46B GLU* 3.0 12.4 + - + +
712J LEU* 4.6 26.9 - - + -
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Residues in contact with ILE 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B THR* 3.6 33.0 - - + +
19B ALA* 4.3 8.1 - - + -
23B ARG* 3.9 14.8 - - - +
41B GLY 3.4 0.4 - - - -
42B LEU* 1.3 85.8 - - + +
44B ALA* 1.3 57.1 + - - +
46B GLU* 3.0 22.9 + - - +
47B LEU* 2.8 54.4 + - + +
1353B NAP 5.6 4.3 - - - +
711J SER* 5.7 1.3 - - - -
712J LEU* 5.9 0.9 - - - +
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Residues in contact with ALA 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B THR* 3.6 17.8 - - + +
36B VAL* 5.5 1.1 - - + -
38B SER 3.7 12.8 - - - +
39B LEU* 3.4 35.7 - - + +
40B LYS 4.1 4.7 - - - +
41B GLY* 3.3 6.8 + - - +
42B LEU 3.3 0.2 - - - -
43B ILE* 1.3 78.8 - - - +
45B GLU* 1.3 58.2 + - - +
47B LEU* 3.2 4.8 + - - +
48B GLN* 2.9 31.9 + - - +
55B LEU* 3.9 6.3 - - - +
1353B NAP 5.2 0.4 + - - +
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Residues in contact with GLU 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B LEU 4.3 5.7 + - - +
41B GLY 3.0 15.9 + - - +
42B LEU* 2.8 41.6 - - + +
44B ALA* 1.3 80.1 - - - +
46B GLU* 1.3 62.2 + - - +
48B GLN* 3.5 10.1 + - - +
49B ALA* 3.2 21.7 + - - +
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Residues in contact with GLU 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B ARG* 2.8 38.4 + - - +
42B LEU* 3.0 14.5 + - + +
43B ILE* 3.0 30.8 + - - +
45B GLU* 1.3 78.0 - - - +
47B LEU* 1.3 62.1 + - - +
49B ALA* 2.9 27.4 + - + +
50B ILE* 3.2 14.6 + - + +
710J LEU 4.2 1.6 - - - +
711J SER* 3.8 6.4 - - - -
712J LEU* 3.8 31.2 + - - +
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Residues in contact with LEU 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B ALA* 3.2 40.8 - - + +
14B THR* 4.2 4.7 - - + +
19B ALA* 4.4 6.3 - - + -
22B ILE* 3.7 22.2 - - + -
23B ARG* 4.6 10.3 - - + +
36B VAL* 5.4 0.9 - - + -
43B ILE* 2.8 35.2 + - + +
44B ALA 3.8 3.1 - - - +
46B GLU* 1.3 76.8 - - + +
48B GLN* 1.3 59.7 + - - +
49B ALA 3.0 5.7 + - - -
50B ILE* 3.4 32.6 + - + +
53B VAL* 3.5 23.8 - - + +
55B LEU* 4.4 15.0 - - + -
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Residues in contact with GLN 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B LEU* 4.1 35.0 - - - +
44B ALA 2.9 15.7 + - - +
45B GLU* 3.9 9.9 - - - +
46B GLU 3.3 0.2 - - - -
47B LEU* 1.3 77.3 - - - +
49B ALA* 1.3 60.7 + - - +
50B ILE 4.5 2.8 - - - +
53B VAL 5.1 6.1 - - - +
55B LEU* 3.8 19.8 - - + +
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Residues in contact with ALA 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B GLU 3.2 12.2 + - - +
46B GLU* 2.9 17.9 + - - +
47B LEU 3.0 0.2 - - - -
48B GLN* 1.3 80.3 - - - +
50B ILE* 1.3 64.0 + - + +
51B PRO* 3.2 8.4 - - - +
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Residues in contact with ILE 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B ILE* 4.3 7.0 - - + -
23B ARG* 4.3 19.7 - - + +
26B ALA* 3.4 31.6 - - + -
27B ALA 5.4 0.2 - - - +
46B GLU* 3.2 13.4 + - + +
47B LEU* 3.4 39.5 + - + +
48B GLN 4.5 1.6 - - - +
49B ALA* 1.3 76.1 - - + +
51B PRO* 1.3 77.7 - - + +
52B ASN 4.6 0.9 - - - +
53B VAL* 3.2 28.7 + - + +
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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