Contacts of the helix formed by residues 28 - 40 (chain C) in PDB entry 1M1P
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 28 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25C SER* 2.9 8.2 + - - -
26C ALA 3.7 1.4 - - - -
27C ASP* 1.3 77.4 - - - +
29C ALA* 1.3 63.8 + - - +
30C PHE 3.4 2.2 - - - -
31C GLU* 3.3 21.6 + - - +
32C PHE* 3.1 23.4 + - - +
57C VAL* 5.6 5.2 - - - +
801C HEC 6.0 6.5 - - - -
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Residues in contact with ALA 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C ASP* 3.1 23.7 + - - +
28C GLY* 1.3 74.3 - - - +
30C PHE* 1.3 66.3 + - - +
32C PHE* 3.3 9.7 + - - +
33C ALA* 3.0 22.5 + - - +
57C VAL* 6.2 0.9 - - - -
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Residues in contact with PHE 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C GLU 5.7 0.2 - - - -
18C CYS 3.6 17.3 - - - -
19C HIS* 4.0 2.2 - - - -
20C LYS* 3.4 55.2 - - + -
25C SER* 4.3 11.3 + - - -
27C ASP* 4.8 0.4 + - - -
28C GLY 3.4 0.6 - - - -
29C ALA* 1.3 77.7 - - - +
31C GLU* 1.3 70.5 + - - +
33C ALA* 3.2 10.6 + - + +
34C GLN* 3.1 46.2 + - + +
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Residues in contact with GLU 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C CYS* 3.4 21.2 - - + +
19C HIS* 2.8 42.7 + - + +
20C LYS 5.1 0.2 + - - -
23C THR 4.1 1.7 - - - +
24C PRO* 3.6 0.6 - - - +
25C SER* 2.6 47.0 + - - -
28C GLY* 3.3 14.5 - - - +
29C ALA 3.2 0.2 - - - -
30C PHE* 1.3 78.5 - - - +
32C PHE* 1.3 56.2 + - - +
34C GLN* 3.1 5.0 + - - +
35C CYS* 3.0 32.6 + - - -
801C HEC 4.1 27.1 - - + -
802C HEC 4.3 1.6 - - + +
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Residues in contact with PHE 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C GLY 3.1 16.8 + - - +
29C ALA* 3.3 8.0 + - - +
31C GLU* 1.3 75.6 - - - +
33C ALA* 1.3 64.0 + - - +
35C CYS* 3.3 7.0 + - - +
36C GLN* 3.2 60.5 + - + -
42C LEU* 4.9 7.0 - - + -
56C LEU 4.1 8.3 - - - -
57C VAL* 3.5 35.7 - - + -
58C CYS* 3.6 44.2 - - - -
59C ALA 6.3 0.2 - - - +
803C HEC 4.4 4.3 - - + -
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Residues in contact with ALA 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C ALA 3.0 12.8 + - - +
30C PHE* 3.2 13.9 + - + +
32C PHE* 1.3 78.9 - - - +
34C GLN* 1.3 58.3 + - + +
36C GLN* 3.4 14.3 + - - +
37C SER* 2.9 26.2 + - - -
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Residues in contact with GLN 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C GLU 4.5 7.7 + - - -
17C SER 3.6 27.3 + - - +
18C CYS* 3.8 16.2 - - + +
30C PHE* 3.1 42.4 + - + +
31C GLU 3.1 7.4 + - - +
33C ALA* 1.3 76.4 - - + +
35C CYS* 1.3 65.1 + - - +
37C SER* 3.1 26.2 + - - -
38C CYS* 3.3 9.5 + - - -
802C HEC 3.4 13.4 - - + +
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Residues in contact with CYS 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C GLU 3.0 19.4 + - - -
32C PHE* 3.3 9.2 + - - +
34C GLN* 1.3 76.7 - - - +
36C GLN* 1.3 59.0 + - - +
38C CYS 3.5 0.2 + - - -
39C HIS* 3.0 35.7 + - - +
58C CYS* 3.5 31.0 - - - -
59C ALA* 5.5 0.7 - - - -
802C HEC 1.9 69.0 - - + +
803C HEC 4.2 2.2 - - + -
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Residues in contact with GLN 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C PHE* 3.2 62.0 + - + +
33C ALA* 3.6 11.3 - - - +
34C GLN 3.1 0.2 - - - -
35C CYS* 1.3 78.5 - - - +
37C SER* 1.3 67.1 + - - +
40C GLY* 2.9 39.6 + - - +
41C LYS* 3.7 29.6 - - + +
42C LEU* 5.2 1.0 + - - +
803C HEC 4.4 7.2 - - + -
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Residues in contact with SER 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C ALA 2.9 14.4 + - - -
34C GLN* 3.1 25.8 + - - -
36C GLN* 1.3 80.1 - - - +
38C CYS* 1.3 64.6 + - - +
40C GLY 4.7 0.5 + - - -
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Residues in contact with CYS 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C GLN* 3.3 3.9 + - - +
36C GLN 3.2 0.2 - - - -
37C SER* 1.3 86.4 - - - +
39C HIS* 1.3 61.3 + - - +
802C HEC 2.4 75.8 - - + -
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Residues in contact with HIS 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C CYS 3.0 21.9 + - - +
38C CYS* 1.3 77.0 + - - +
40C GLY* 1.3 59.7 + - - +
45C MET* 4.2 9.2 - - + +
802C HEC 2.1 90.3 + + + -
803C HEC 3.5 41.9 - - + +
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Residues in contact with GLY 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C GLN* 2.9 34.4 + - - +
37C SER 4.7 0.4 + - - -
38C CYS 3.6 0.6 - - - -
39C HIS* 1.3 80.2 - - - +
41C LYS* 1.3 63.2 + - - -
45C MET* 3.4 14.7 - - - +
803C HEC 4.1 2.8 - - - +
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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