Contacts of the helix formed by residues 26 - 39 (chain A) in PDB entry 1MDF
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 THR 26 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A GLU* 1.3 76.1 - - - +
27A PHE* 1.3 61.0 + - - +
28A GLY* 3.2 6.2 + - - -
29A ASP* 2.5 40.1 + - - +
30A LEU* 2.9 26.5 + - - +
179A VAL* 3.0 43.3 - - + +
180A LYS 3.7 1.1 - - - +
181A SER* 3.5 20.9 - - - +
204A HIS* 3.5 16.2 - - + -
208A ILE* 3.6 4.6 - - - +
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Residues in contact with PHE 27 (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 THR* 1.3 72.4 - - - +
28A GLY* 1.3 65.0 + - - +
30A LEU* 3.5 11.1 - - + +
31A LEU* 3.0 21.0 + - - +
93A PHE* 3.6 24.1 - + + -
96A PHE* 3.4 43.7 - + + -
185A ALA* 4.0 15.3 - - + -
186A PHE* 4.3 7.0 - + - -
204A HIS* 3.2 37.2 + + - +
207A TYR* 3.6 28.0 - + + -
208A ILE* 3.8 28.0 - - + -
211A LEU* 4.0 18.8 - - + -
244A LEU* 4.5 11.0 - - + -
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Residues in contact with GLY 28 (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 THR* 3.1 7.4 + - - -
27A PHE* 1.3 80.8 - - - +
29A ASP* 1.3 60.0 + - - +
31A LEU* 5.0 0.4 - - - -
32A ARG* 3.2 14.7 + - - +
93A PHE* 5.1 2.7 - - - -
96A PHE* 4.7 6.1 + - - +
97A ARG* 3.1 47.7 + - - -
204A HIS* 5.1 0.4 - - - -
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Residues in contact with ASP 29 (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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24A GLY 4.5 2.1 - - - +
25A GLU* 3.4 18.1 - - + +
26A THR* 2.5 46.1 + - - +
28A GLY* 1.3 76.1 - - - +
30A LEU* 1.3 65.1 + - - +
32A ARG* 3.4 5.7 + - - +
33A ASP* 3.0 27.5 + - - +
179A VAL 5.0 0.2 - - - +
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Residues in contact with LEU 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A GLU* 4.7 9.6 - - - +
26A THR 2.9 13.4 + - - +
27A PHE* 3.5 20.9 - - + +
29A ASP* 1.3 78.1 - - - +
31A LEU* 1.3 59.0 + - - +
33A ASP* 3.4 0.4 + - - -
34A ARG* 2.9 73.2 + - + +
93A PHE* 5.3 5.2 - - + -
208A ILE* 4.4 20.2 - - + -
211A LEU* 4.9 4.0 - - + -
244A LEU 5.8 0.2 - - - +
247A LEU* 5.1 2.9 - - + -
248A TYR* 3.6 37.0 - - + +
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Residues in contact with LEU 31 (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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27A PHE 3.0 15.9 + - - +
28A GLY 4.3 2.2 - - - +
30A LEU* 1.3 75.2 - - - +
32A ARG* 1.3 60.8 + - - +
34A ARG* 4.5 3.1 - - + +
35A ALA* 2.8 34.6 + - + +
53A TYR* 4.1 19.7 - - + +
56A LEU* 3.7 37.0 - - + -
57A ASP* 3.8 27.6 - - - +
60A ALA* 4.2 7.0 - - + -
93A PHE* 3.6 41.7 - - + -
97A ARG* 4.4 4.7 - - - +
247A LEU* 5.9 1.6 - - + -
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Residues in contact with ARG 32 (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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28A GLY 3.2 19.1 + - - +
29A ASP* 3.6 6.7 - - - +
31A LEU* 1.3 76.5 - - - +
33A ASP* 1.3 60.0 + - - +
35A ALA* 3.6 1.9 - - - +
36A ALA* 2.9 32.1 + - + +
57A ASP* 3.4 25.6 + - - +
61A ASP* 2.5 42.8 + - - -
97A ARG* 3.5 20.6 - - - +
176A LEU* 6.0 2.0 - - - +
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Residues in contact with ASP 33 (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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25A GLU* 6.1 1.3 - - - +
29A ASP 3.0 15.3 + - - +
30A LEU* 3.7 2.7 - - - +
32A ARG* 1.3 81.4 - - - +
34A ARG* 1.3 85.8 + - - +
36A ALA* 3.4 6.5 + - - +
37A LYS* 2.8 49.2 + - - +
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Residues in contact with ARG 34 (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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25A GLU* 4.6 8.5 + - - -
30A LEU* 2.9 61.3 + - + +
31A LEU* 4.0 4.0 - - - +
33A ASP* 1.3 93.5 + - - +
35A ALA* 1.3 58.5 + - - +
37A LYS* 4.2 3.6 - - - -
38A TYR* 2.5 77.9 + - + +
53A TYR* 4.0 13.9 - - + -
247A LEU* 4.2 6.1 - - + +
248A TYR* 2.9 62.0 + - - -
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Residues in contact with ALA 35 (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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31A LEU 2.8 21.4 + - - +
32A ARG 3.6 0.9 - - - +
34A ARG* 1.3 72.6 - - - +
36A ALA* 1.3 57.6 + - - +
39A GLY* 2.7 31.0 + - - -
53A TYR* 3.7 22.3 - - + +
54A ARG* 3.4 16.5 - - + +
57A ASP* 3.3 36.1 - - + +
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Residues in contact with ALA 36 (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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32A ARG* 2.9 18.8 + - + +
33A ASP* 3.7 7.0 - - - +
35A ALA* 1.3 76.4 - - - +
37A LYS* 1.3 62.3 + - + +
54A ARG* 3.7 23.5 + - - +
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Residues in contact with LYS 37 (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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33A ASP* 2.8 39.1 + - - +
34A ARG* 3.7 4.3 - - - +
36A ALA* 1.3 80.9 - - + +
38A TYR* 1.3 94.3 + - + +
41A ARG* 5.1 0.9 + - - -
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Residues in contact with TYR 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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34A ARG* 2.5 66.3 + - + +
37A LYS* 1.3 108.4 + - - +
39A GLY* 1.3 63.5 + - - +
40A ASP 2.9 4.2 + - - -
41A ARG* 3.0 58.0 + - - +
53A TYR* 4.0 22.2 - + + -
247A LEU 4.4 0.4 - - - -
248A TYR 4.1 2.3 + - - -
249A ALA* 4.2 3.5 + - - -
250A GLY* 3.4 33.2 + - - -
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Residues in contact with GLY 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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35A ALA* 2.7 27.8 + - - +
36A ALA 4.4 0.2 + - - -
37A LYS 3.6 1.4 - - - -
38A TYR* 1.3 71.0 - - - +
40A ASP* 1.3 60.8 + - - -
41A ARG 3.3 1.2 + - - -
52A SER* 3.5 0.5 - - - -
53A TYR 3.5 5.2 + - - -
54A ARG* 2.9 54.7 + - - +
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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