Contacts of the helix formed by residues 38 - 48 (chain B) in PDB entry 1E7K
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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36B ARG 4.2 0.2 + - - -
37B LYS* 1.3 74.4 - - - +
39B ALA* 1.3 56.5 + - - -
40B ASN 3.1 3.7 + - - -
41B GLU 3.2 2.3 + - - -
42B ALA* 2.7 34.0 + - - +
101B ALA 2.6 18.0 + - - -
30D A 3.4 14.4 + - - -
31D U 3.2 12.1 - - - -
32D G 3.2 8.5 - - - -
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Residues in contact with ALA 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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38B GLY* 1.3 69.6 - - - +
40B ASN* 1.3 54.7 + - - +
42B ALA* 3.3 7.9 - - - +
43B THR* 2.7 40.3 + - - -
65B ILE* 4.8 5.8 - - + +
66B ILE* 4.0 25.8 - - + -
68B HIS* 4.6 13.0 - - + -
69B LEU* 4.6 2.1 - - + +
100B ILE* 4.2 3.2 - - + +
101B ALA* 3.8 7.8 + - - -
31D U 2.7 21.0 + - - +
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Residues in contact with ASN 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 3.1 0.4 - - - -
39B ALA* 1.3 83.3 - - - +
41B GLU* 1.3 65.8 + - - +
43B THR* 2.9 14.2 + - - -
44B LYS* 3.0 19.7 + - + +
31D U 4.7 1.7 + - - -
32D G 3.4 33.3 + - - +
43D G 3.6 22.4 + - - +
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Residues in contact with GLU 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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36B ARG* 3.4 38.6 + - + +
37B LYS* 3.2 15.1 + - - +
38B GLY 3.2 1.2 + - - -
40B ASN* 1.3 78.4 - - - +
42B ALA* 1.3 64.9 + - - +
44B LYS* 3.3 12.7 + - + +
45B THR* 2.9 27.3 + - - +
30D A 4.2 1.4 - - - +
32D G 2.5 43.2 + - - +
43D G 3.1 50.7 - - + +
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Residues in contact with ALA 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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36B ARG* 4.8 2.1 + - - +
38B GLY 2.7 22.8 + - - +
39B ALA* 3.3 9.9 - - - +
41B GLU* 1.3 71.7 - - - +
43B THR* 1.3 64.0 + - - +
45B THR* 2.4 28.1 + - - -
46B LEU* 3.2 8.2 + - - +
54B ILE* 4.7 9.6 - - + -
69B LEU* 4.8 5.2 - - + -
101B ALA* 4.6 3.1 - - + +
102B CYS* 4.3 13.9 - - - +
103B SER* 3.9 24.0 - - - +
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Residues in contact with THR 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 ALA 2.7 15.9 + - - -
40B ASN* 3.2 11.2 - - - +
42B ALA* 1.3 72.9 - - - +
44B LYS* 1.3 67.0 + - + +
46B LEU* 2.9 18.7 + - - +
47B ASN* 3.0 29.0 + - - +
68B HIS* 3.1 30.1 + - + +
69B LEU* 3.4 11.6 - - - +
72B LEU* 4.1 10.1 - - + -
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Residues in contact with LYS 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 ASN* 3.0 20.8 + - + +
41B GLU* 3.3 13.4 + - - +
43B THR* 1.3 80.6 - - + +
45B THR* 1.3 55.5 + - + +
47B ASN* 3.2 7.9 + - - +
48B ARG* 2.7 68.9 + - - +
41D C 4.0 22.7 + - - +
42D C 3.4 28.3 + - - -
43D G 3.0 40.8 + - - +
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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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36B ARG* 3.7 33.7 - - + -
41B GLU 2.9 18.2 + - - +
42B ALA 2.4 22.3 + - - +
44B LYS* 1.3 75.5 - - - +
46B LEU* 1.3 61.8 + - - +
49B GLY 3.0 7.6 + - - -
50B ILE* 2.9 51.1 + - + +
51B SER* 3.4 10.7 + - - -
54B ILE* 4.0 0.9 - - - +
103B SER* 2.8 27.0 + - - +
105B THR* 4.8 3.1 - - - +
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Residues in contact with LEU 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 ALA 3.8 4.7 - - - +
43B THR* 2.9 7.5 + - - +
45B THR* 1.3 82.4 + - - +
47B ASN* 1.3 54.1 + - - +
49B GLY* 2.7 26.0 + - - -
51B SER* 3.8 12.1 - - - +
54B ILE* 3.6 35.2 - - + -
69B LEU* 3.9 25.1 - - + -
72B LEU* 3.6 32.1 - - + +
73B CYS* 4.1 17.7 - - - -
76B LYS* 3.6 18.0 - - + +
78B VAL* 3.9 25.0 - - + +
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Residues in contact with ASN 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 THR* 3.0 32.0 + - - +
44B LYS* 3.8 9.0 - - - +
46B LEU* 1.3 76.3 - - - +
48B ARG* 1.3 61.4 + - + +
49B GLY* 3.4 0.7 + - - -
72B LEU* 3.5 26.4 - - - +
76B LYS* 4.2 18.1 - - - +
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Residues in contact with ARG 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 LYS* 2.7 59.2 + - - +
47B ASN* 1.3 73.7 - - - +
49B GLY* 1.3 63.0 + - - +
50B ILE* 3.5 30.8 + - + +
41D C 3.6 21.6 + - - -
42D C 3.4 30.5 + - - -
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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