Contacts of the helix formed by residues 42 - 48 (chain B) in PDB entry 3DVA
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 42 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14B ARG* 4.5 7.6 + - - -
31B GLY 5.7 1.2 + - - -
34B GLY* 5.2 1.0 - - - -
40B THR 3.4 1.6 + - - -
41B GLU* 1.3 75.9 - - - +
43B LEU* 1.3 64.4 + - - +
44B GLN 3.4 2.5 - - - -
45B ALA* 3.4 13.7 + - - +
46B GLU* 3.1 24.4 + - - +
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Residues in contact with LEU 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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10B THR* 4.3 6.3 - - + +
13B LEU* 4.0 23.3 - - + -
14B ARG* 3.9 48.2 - - + +
17B LEU* 4.0 12.3 - - + -
25B ILE* 5.0 4.5 - - + -
39B ALA 4.2 2.2 - - - +
40B THR* 3.4 42.1 + - + +
41B GLU 3.2 2.4 - - - +
42B GLY* 1.3 74.9 - - - +
44B GLN* 1.3 61.8 + - - +
46B GLU* 3.3 0.9 + - - -
47B PHE* 2.9 38.9 + - + +
52B VAL* 4.0 16.5 - - + +
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Residues in contact with GLN 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B GLY* 3.7 21.6 - - - +
32B VAL* 3.1 39.4 + - - +
40B THR 4.6 1.6 + - - -
42B GLY 3.4 0.4 - - - -
43B LEU* 1.3 77.8 - - - +
45B ALA* 1.3 58.9 - - - +
48B GLY* 2.7 38.6 + - - +
49B GLU* 3.9 24.8 - - + +
52B VAL* 2.8 45.3 + - + +
53B PHE* 4.1 4.2 - - - +
54B ASP* 4.9 2.6 + - - +
212C LYS* 6.1 2.6 - - - +
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Residues in contact with ALA 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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42B GLY* 3.4 15.8 + - - +
43B LEU 3.3 0.4 - - - -
44B GLN* 1.3 80.3 - - - +
46B GLU* 1.3 59.0 + - - +
48B GLY* 4.6 1.0 + - - -
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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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14B ARG* 2.5 40.3 + - - +
18B LYS* 5.3 6.1 - - - +
42B GLY 3.1 15.9 + - - +
45B ALA* 1.3 79.6 - - - +
47B PHE* 1.3 92.4 + - + +
48B GLY 3.7 0.2 - - - -
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Residues in contact with PHE 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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14B ARG* 3.4 31.6 - - + -
17B LEU* 3.6 33.4 - - + -
18B LYS* 3.6 31.6 - - + -
43B LEU* 2.9 22.2 + - + +
46B GLU* 1.3 116.2 - - + +
48B GLY* 1.3 61.9 + - - +
50B ASP* 4.4 3.6 - - - +
51B ARG* 3.9 41.7 - - + +
52B VAL* 4.8 1.3 - - + -
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Residues in contact with GLY 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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44B GLN* 2.7 26.8 + - - +
45B ALA 4.6 1.0 + - - -
46B GLU 3.7 1.0 - - - -
47B PHE* 1.3 77.0 - - - +
49B GLU* 1.3 61.0 + - - -
50B ASP* 3.3 8.1 - - - -
51B ARG 3.5 1.6 + - - -
52B VAL* 3.2 26.3 + - - +
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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