Contacts of the helix formed by residues 34 - 43 (chain B) in PDB entry 4IA8
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 34 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28B ALA* 4.6 0.4 - - - -
33B LEU* 1.3 77.4 - - - +
35B ARG* 1.3 65.5 + - - +
36B THR* 3.3 22.3 + - - +
37B ALA* 3.2 11.4 + - + +
38B ILE* 3.0 18.9 + - - +
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Residues in contact with ARG 35 (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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24B GLN* 4.1 10.2 + - + +
25B GLU* 3.4 57.4 + - + +
28B ALA* 3.6 15.2 - - + +
34B ASP* 1.3 72.9 - - - +
36B THR* 1.3 57.3 + - + +
38B ILE* 3.2 4.7 + - - +
39B SER* 2.9 31.5 + - - -
101B SO4 3.1 39.8 + - - -
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Residues in contact with THR 36 (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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34B ASP* 3.3 20.3 + - - +
35B ARG* 1.3 76.0 - - + +
37B ALA* 1.3 60.3 + - - -
39B SER* 3.4 6.2 + - - -
40B GLY* 3.0 26.0 + - - -
43B ARG* 4.6 3.4 + - - +
46B ARG* 4.1 10.6 + - - -
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Residues in contact with ALA 37 (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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33B LEU* 4.4 10.5 - - + -
34B ASP* 3.2 26.7 + - + +
36B THR* 1.3 79.4 + - - +
38B ILE* 1.3 64.2 + - - +
40B GLY 3.3 0.7 + - - -
41B ILE* 2.9 34.1 + - + +
46B ARG* 3.5 31.3 - - - +
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Residues in contact with ILE 38 (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 ILE* 5.9 1.1 - - + -
17B ARG* 5.1 0.2 - - - -
24B GLN* 4.2 26.9 - - + +
27B LEU* 3.9 37.9 - - + -
28B ALA* 3.8 21.5 - - + -
31B SER* 4.6 0.7 - - - +
33B LEU* 4.0 18.8 - - + +
34B ASP 3.0 13.9 + - - +
35B ARG* 3.2 7.4 + - - +
37B ALA* 1.3 74.9 - - - +
39B SER* 1.3 58.4 + - - +
41B ILE* 3.2 6.2 + - - +
42B GLU* 2.9 37.8 + - + +
56B ILE* 4.4 17.5 - - + -
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Residues in contact with SER 39 (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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24B GLN* 3.6 27.8 + - - +
35B ARG* 2.9 18.0 + - - -
36B THR* 3.7 6.5 - - - -
38B ILE* 1.3 78.6 - - - +
40B GLY* 1.3 57.0 + - - +
42B GLU* 3.3 3.3 + - - +
43B ARG* 2.8 53.3 + - - +
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Residues in contact with GLY 40 (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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36B THR 3.0 15.2 + - - -
37B ALA 3.7 2.7 - - - -
38B ILE 3.3 0.2 - - - -
39B SER* 1.3 78.5 - - - +
41B ILE* 1.3 59.3 + - - +
43B ARG* 3.1 8.5 + - - +
44B ASN 3.1 2.9 + - - -
45B SER* 3.0 44.1 + - - -
46B ARG* 3.4 16.0 + - - -
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Residues in contact with ILE 41 (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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6B LEU* 5.5 4.6 - - + +
9B VAL* 5.8 0.4 - - + -
10B SER* 3.0 28.7 + - - +
13B ILE* 3.9 28.9 - - + -
33B LEU* 4.5 8.5 - - + -
37B ALA* 2.9 30.6 + - + +
38B ILE* 3.2 8.5 + - - +
40B GLY* 1.3 74.4 - - - +
42B GLU* 1.3 63.4 + - + +
44B ASN* 3.3 7.6 + - - -
46B ARG* 3.8 23.3 - - - +
47B ASN 4.0 12.3 - - - +
48B LEU* 3.6 31.9 - - + -
56B ILE* 4.1 12.3 - - + -
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Residues in contact with GLU 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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10B SER* 3.1 20.4 + - - +
13B ILE* 4.2 14.0 - - + +
14B LYS* 3.4 46.3 + - + +
17B ARG* 2.8 36.4 + - - -
24B GLN* 2.6 31.2 + - - +
38B ILE* 2.9 22.8 + - + +
39B SER 3.8 4.0 - - - +
41B ILE* 1.3 80.3 - - + +
43B ARG* 1.3 57.5 + - - +
44B ASN* 3.1 6.1 + - - -
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Residues in contact with ARG 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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36B THR* 4.6 3.2 + - - +
39B SER* 2.8 38.5 + - - +
40B GLY* 3.1 14.6 + - - +
42B GLU* 1.3 77.1 - - - +
44B ASN* 1.3 64.9 + - - +
45B SER* 2.9 39.7 + - - +
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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