Contacts of the helix formed by residues 38 - 48 (chain B) in PDB entry 5B6Q
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 38 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34B ARG 3.9 0.2 + - - -
35B ILE 3.0 13.6 + - - -
36B ALA 3.2 2.6 + - - -
37B GLN* 1.3 78.0 - - - +
39B LEU* 1.3 63.6 + - - -
40B ASP 3.3 2.7 - - - -
41B THR* 2.7 26.0 + - - -
42B LEU* 3.4 9.8 + - - +
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Residues in contact with LEU 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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35B ILE* 3.7 35.9 + - + +
38B GLY* 1.3 71.9 - - - -
40B ASP* 1.3 58.6 + - - +
42B LEU* 3.0 7.8 + - + +
43B VAL* 2.9 32.7 + - + +
68B LYS* 3.4 46.7 - - + +
71B ILE* 3.9 24.9 - - + -
72B GLU* 3.4 22.9 - - + +
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Residues in contact with ASP 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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38B GLY 3.3 1.0 - - - -
39B LEU* 1.3 79.2 - - - +
41B THR* 1.3 63.7 + - + +
43B VAL* 3.5 10.2 + - - +
44B SER* 3.1 22.3 + - - -
68B LYS* 4.5 18.9 - - - +
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Residues in contact with THR 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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37B GLN* 3.2 31.3 + - - +
38B GLY* 2.7 20.3 + - - +
40B ASP* 1.3 76.4 - - + +
42B LEU* 1.3 67.4 + - - +
44B SER* 3.3 8.4 + - - -
45B THR* 3.2 24.9 + - - -
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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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31B TRP* 4.8 0.4 - - + -
34B ARG* 3.3 44.4 - - + +
35B ILE* 4.3 9.6 - - + +
37B GLN* 4.4 9.2 - - - +
38B GLY 3.6 12.3 - - - +
39B LEU* 3.0 11.1 + - - +
41B THR* 1.3 86.5 + - - +
43B VAL* 1.3 61.4 + - - +
45B THR* 3.3 8.3 + - - -
46B VAL* 3.2 27.9 + - - +
71B ILE* 3.8 27.6 - - + -
101B HEC 4.0 41.4 - - + +
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Residues in contact with VAL 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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39B LEU 2.9 21.0 + - - +
40B ASP* 3.6 14.1 - - - +
41B THR 3.3 0.2 - - - -
42B LEU* 1.3 76.3 - - - +
44B SER* 1.3 63.7 + - - +
46B VAL* 3.3 8.1 + - - +
47B LYS* 3.1 39.4 + - + +
64B ASP* 3.9 25.1 - - + +
67B TYR* 4.0 11.4 - - + -
68B LYS* 3.7 37.7 - - + +
71B ILE* 4.7 4.3 - - + -
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Residues in contact with SER 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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40B ASP 3.1 14.0 + - - -
41B THR* 3.5 11.2 - - - -
42B LEU 3.3 0.2 - - - -
43B VAL* 1.3 76.5 - - - +
45B THR* 1.3 62.5 + - - +
47B LYS* 3.1 13.0 + - - +
48B THR* 3.0 33.8 + - - +
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Residues in contact with THR 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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41B THR 3.2 11.8 + - - -
42B LEU* 3.3 12.3 + - - -
44B SER* 1.3 77.5 - - - +
46B VAL* 1.3 57.5 + - + +
48B THR* 2.9 28.7 + - - +
50B LYS* 3.8 34.4 + - + +
101B HEC 4.2 30.1 + - + +
102B IMD 3.6 14.2 + - + +
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Residues in contact with VAL 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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42B LEU 3.2 16.1 + - - +
43B VAL* 3.6 6.7 - - - +
44B SER 3.2 0.6 - - - -
45B THR* 1.3 74.3 - - - +
47B LYS* 1.3 58.4 + - - +
48B THR 3.2 6.1 - - - +
56B GLY 2.8 36.9 + - - -
57B GLY* 4.0 3.6 - - - +
67B TYR* 3.7 34.1 - - + -
71B ILE* 4.1 5.6 - - + -
101B HEC 3.3 53.4 - - + -
102B IMD 3.8 13.0 - - + -
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Residues in contact with LYS 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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43B VAL* 3.1 25.2 + - + +
44B SER* 3.1 9.6 + - - +
46B VAL* 1.3 76.9 - - - +
48B THR* 1.3 62.8 + - + +
55B PRO* 3.5 9.0 - - - +
56B GLY* 3.4 18.9 + - - +
64B ASP* 2.6 39.1 + - - +
67B TYR* 3.4 24.5 - - + -
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Residues in contact with THR 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 SER* 3.0 24.3 + - - +
45B THR* 2.9 24.6 + - - +
46B VAL 3.2 7.6 - - - +
47B LYS* 1.3 80.1 - - + +
49B GLY* 1.3 60.2 + - - +
50B LYS* 2.9 17.9 + - - +
55B PRO* 3.8 3.3 - - - +
102B IMD 4.6 3.3 - - - -
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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