Contacts of the strand formed by residues 43 - 54 (chain C) in PDB entry 5IXM
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 43 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37C HIS 3.7 1.6 - - - +
38C TYR* 3.8 6.5 - - - -
39C MET* 2.9 40.7 + - - +
42C ARG* 1.3 78.2 - - - +
44C LEU* 1.3 60.9 + - - -
66C LEU* 3.7 9.2 - - - -
68C ASN 4.4 3.1 - - - -
70C ARG* 3.9 14.3 - - - +
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Residues in contact with LEU 44 (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 PRO* 4.2 11.7 - - + -
37C HIS 3.8 18.6 - - - +
38C TYR* 4.0 16.8 - - + +
43C GLY* 1.3 73.3 - - - -
45C GLN* 1.3 68.8 + - - +
46C TRP* 3.8 35.5 + - + +
66C LEU* 3.4 4.1 - - - +
67C PRO* 3.2 26.9 - - + +
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Residues in contact with GLN 45 (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 PRO* 3.5 4.9 - - - +
37C HIS* 2.9 48.1 + - + +
39C MET* 3.8 12.3 - - + -
43C GLY 3.8 0.2 + - - -
44C LEU* 1.3 76.6 - - - +
46C TRP* 1.3 68.4 + - - +
47C GLN* 2.4 37.7 + - - +
64C ASP* 3.9 6.1 + - - +
65C TRP 3.5 16.3 - - - +
66C LEU* 3.7 13.1 - - + +
84C ARG 5.5 0.4 + - - -
113C TYR* 3.4 24.7 + - - -
117C LEU* 3.7 28.7 - - - +
118C THR 5.4 0.8 + - - -
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Residues in contact with TRP 46 (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 ILE* 3.9 25.4 - - + -
35C THR 3.6 2.0 - - - -
36C PRO* 3.5 33.0 - - + -
44C LEU* 3.8 36.0 + - + +
45C GLN* 1.3 79.2 - - - +
47C GLN* 1.3 61.5 + - - +
48C ASN* 4.0 12.1 + - - +
63C LEU 3.5 2.8 - - - +
64C ASP* 3.3 4.2 - - - -
65C TRP* 2.9 70.2 + + + +
67C PRO* 5.0 2.5 - - + +
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Residues in contact with GLN 47 (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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19C LEU* 4.8 7.5 - - - +
33C THR* 3.3 5.4 - - - +
35C THR* 2.9 49.4 + - - +
37C HIS* 3.9 21.2 + - + -
45C GLN* 2.4 36.5 + - + +
46C TRP* 1.3 74.8 - - - +
48C ASN* 1.3 61.2 + - - +
49C GLU* 5.7 0.2 - - - -
64C ASP* 3.4 29.4 + - - +
118C THR 3.7 17.0 + - - +
119C SER* 6.2 0.4 - - - -
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Residues in contact with ASN 48 (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 THR 3.2 5.4 - - - +
34C ILE* 3.3 35.1 - - + +
46C TRP* 4.1 14.2 + - - +
47C GLN* 1.3 75.6 + - - +
49C GLU* 1.3 62.6 + - - +
50C PHE* 5.8 0.2 - - - -
62C ALA* 3.2 6.9 - - - +
63C LEU* 3.0 54.7 + - + +
64C ASP* 4.2 1.7 + - - +
65C TRP* 5.5 3.0 - - - +
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Residues in contact with GLU 49 (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 ASP 3.9 0.2 - - - +
32C ALA* 3.1 6.2 - - - -
33C THR* 2.9 52.1 + - + +
47C GLN 5.6 0.2 - - - +
48C ASN* 1.3 74.8 - - - +
50C PHE* 1.3 62.2 + - - +
51C ARG* 4.1 18.2 + - + +
60C THR* 3.6 20.7 - - + +
61C MET 3.5 4.0 - - - +
62C ALA* 5.0 2.9 - - + -
120C GLN* 4.4 11.3 + - - +
121C TYR* 3.0 25.0 + - - +
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Residues in contact with PHE 50 (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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26C ILE* 5.0 5.8 - - + -
30C PHE* 3.5 40.8 - + + -
31C ASP 3.1 24.9 - - - -
32C ALA* 4.4 8.7 - - + +
48C ASN 4.3 0.4 - - - -
49C GLU* 1.3 74.4 - - - +
51C ARG* 1.3 65.8 + - - +
52C TYR* 4.1 18.2 + + + -
59C GLY 4.0 0.2 - - - +
60C THR* 3.4 3.2 - - - -
61C MET* 2.9 63.4 + - + +
604C C8E 4.2 31.0 - - + -
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Residues in contact with ARG 51 (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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23C TYR* 4.9 6.5 + - - -
30C PHE* 3.6 3.5 - - - -
31C ASP* 2.8 70.1 + - + +
49C GLU* 4.1 19.0 - - + +
50C PHE* 1.3 77.4 - - - +
52C TYR* 1.3 61.4 + - - +
59C GLY 3.5 5.2 - - - +
60C THR* 3.8 22.7 - - + +
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Residues in contact with TYR 52 (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 ASN 3.5 5.4 - - - -
30C PHE* 3.9 24.7 - - + -
50C PHE* 4.1 21.1 - + + -
51C ARG* 1.3 76.2 - - - +
53C LEU* 1.3 64.3 + - - +
54C LEU* 4.2 14.1 - - + -
57C GLY 3.9 6.1 - - - -
58C SER* 3.4 4.3 - - - -
59C GLY* 2.9 55.6 + - - +
60C THR 3.8 1.6 - - - -
61C MET* 4.5 10.8 - - + -
89C TRP* 2.8 34.0 + + - -
91C HIS* 2.6 42.1 + + - +
604C C8E 4.0 14.0 - - - -
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Residues in contact with LEU 53 (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 ASN* 3.2 41.1 + - + +
52C TYR* 1.3 76.3 - - - +
54C LEU* 1.3 82.7 + - - +
57C GLY* 4.0 1.8 - - - -
58C SER* 3.8 22.9 - - - +
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Residues in contact with LEU 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C ASN* 5.1 2.2 - - + +
30C PHE* 3.6 28.0 - - + -
52C TYR* 4.2 16.4 - - + -
53C LEU* 1.3 91.1 - - - +
55C ALA* 1.3 61.7 + - - +
56C PRO* 3.4 12.8 - - + -
57C GLY* 2.9 30.5 + - - +
604C C8E 3.6 55.0 - - - +
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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