Contacts of the helix formed by residues 37 - 48 (chain A) in PDB entry 4K8T
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 37 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A ILE* 1.3 76.2 - - - +
38A ALA* 1.3 59.4 + - - +
39A GLU* 3.3 13.2 + - - +
40A ARG* 2.9 33.1 + - - +
41A ALA* 2.9 28.1 + - - +
128A TYR* 3.9 7.0 - - - -
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Residues in contact with ALA 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A ASP* 1.3 76.6 - - - +
39A GLU* 1.3 61.9 + - - +
41A ALA* 3.4 2.4 + - - +
42A GLU* 3.2 29.0 + - + +
128A TYR* 3.8 16.1 - - + +
402A E34 3.8 39.2 - - + +
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Residues in contact with GLU 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A ASP* 3.2 11.3 + - - +
38A ALA* 1.3 77.4 - - - +
40A ARG* 1.3 58.0 + - - +
42A GLU* 3.4 9.3 + - + +
43A LEU* 3.0 28.2 + - + +
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Residues in contact with ARG 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A ASN* 2.7 31.7 + - - -
27A GLN* 4.3 6.4 + - - +
28A ILE* 3.9 17.4 - - - +
34A ASN* 6.4 0.2 - - - +
36A ILE* 3.6 32.4 - - + +
37A ASP* 2.9 23.1 + - - +
39A GLU* 1.3 74.7 - - - +
41A ALA* 1.3 60.9 + - - +
43A LEU* 3.6 24.1 - - - +
44A LEU* 2.9 50.8 + - + +
126A ASN* 4.8 1.8 + - - -
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Residues in contact with ALA 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A ILE* 3.7 13.9 - - + +
37A ASP 2.9 17.4 + - - +
38A ALA* 3.6 0.4 - - - +
39A GLU 3.2 0.4 - - - -
40A ARG* 1.3 74.1 - - - +
42A GLU* 1.3 64.1 + - - +
45A TYR* 3.0 23.6 + - - +
112A ARG* 5.3 0.2 - - - -
114A MSE 3.1 19.5 - - + +
128A TYR* 4.3 7.2 - - + -
402A E34 3.5 26.7 - - + -
403A DMS 3.6 10.8 - - - +
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Residues in contact with GLU 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A ALA* 3.2 15.2 + - + +
39A GLU* 3.6 9.6 - - + +
41A ALA* 1.3 74.8 - - - +
43A LEU* 1.3 65.9 + - - +
45A TYR* 3.3 3.6 + - - +
46A SER* 3.0 24.9 + - - -
402A E34 3.7 21.1 - - + +
403A DMS 3.6 24.0 - - + +
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Residues in contact with LEU 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A ASN* 6.0 0.2 - - - +
39A GLU* 3.0 16.0 + - + +
40A ARG* 3.6 28.5 - - + +
41A ALA 3.3 0.2 - - - -
42A GLU* 1.3 75.6 - - - +
44A LEU* 1.3 64.6 + - + +
46A SER* 2.5 31.0 + - - +
47A ARG* 3.4 35.6 + - - +
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Residues in contact with LEU 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A PHE* 5.0 4.9 - - + -
26A ASN* 4.0 19.7 - - - +
28A ILE* 4.1 14.6 - - + -
36A ILE* 4.3 5.4 - - + -
40A ARG* 2.9 63.6 + - + +
43A LEU* 1.3 75.2 - - + +
45A TYR* 1.3 57.9 + - - +
47A ARG* 3.2 7.2 + - - +
48A MSE 3.0 27.4 + - - +
114A MSE 3.8 14.5 - - + +
116A PHE* 4.4 8.3 - - + -
126A ASN* 3.7 39.3 - - + +
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Residues in contact with TYR 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A ILE* 3.8 22.5 - - + +
41A ALA 3.0 18.8 + - - +
42A GLU* 3.7 6.1 - - - +
44A LEU* 1.3 76.2 - - - +
46A SER* 1.3 60.4 + - - +
48A MSE 3.1 11.9 + - - -
53A GLU* 4.7 2.8 + - - -
114A MSE 3.6 19.2 - - - -
403A DMS 3.7 36.1 - - + -
86B ASP* 4.4 11.0 - - + -
87B ILE* 3.6 26.5 + - - +
90B HIS* 2.8 79.8 - + + +
91B ASP* 4.6 1.6 + - - -
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Residues in contact with SER 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A GLU 3.0 13.3 + - - -
43A LEU* 2.5 28.2 + - - +
45A TYR* 1.3 78.5 - - - +
47A ARG* 1.3 61.6 + - - +
48A MSE 4.7 1.7 - - - +
90B HIS* 5.0 3.4 - - - -
94B ALA* 6.0 0.7 - - - +
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Residues in contact with ARG 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A PHE* 3.6 25.0 - - + -
25A ASP* 4.5 11.1 + - - +
26A ASN* 2.8 41.1 + - - +
43A LEU* 3.6 37.8 - - - +
44A LEU* 3.2 9.8 + - - +
45A TYR 3.1 0.4 - - - -
46A SER* 1.3 82.4 - - - +
48A MSE 1.3 64.2 + - - +
49A GLY 3.8 1.2 + - - -
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Residues in contact with MSE 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A ILE* 3.2 46.9 - - - +
15A ILE 4.2 0.2 - - - -
16A SER* 3.7 20.4 - - - +
22A PHE* 4.7 0.2 - - - -
44A LEU 3.0 11.5 + - - +
45A TYR* 3.1 21.4 + - - +
46A SER 4.7 1.6 - - - +
47A ARG* 1.3 81.6 - - - +
49A GLY* 1.3 70.3 + - - +
51A ALA* 4.4 4.0 - - - -
114A MSE 3.8 20.4 - - + +
115A ILE 3.8 8.7 - - - +
116A PHE* 3.6 37.5 - - + -
90B HIS* 3.0 21.3 - - + -
94B ALA* 3.5 7.6 - - - +
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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