Contacts of the helix formed by residues 25 - 38 (chain C) in PDB entry 5I4A
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 GLU 25 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24C MET* 1.3 77.7 - - - +
26C PRO* 1.3 78.0 - - + +
27C LYS* 3.2 7.3 + - + +
28C LEU* 3.3 13.9 + - + +
29C PHE* 2.9 21.0 + - - +
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Residues in contact with PRO 26 (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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20C TYR* 5.9 0.9 - - + -
21C ASN 5.9 1.6 - - - +
24C MET 3.9 4.9 - - - +
25C GLU* 1.3 94.0 - - + +
27C LYS* 1.3 58.4 + - - +
29C PHE* 4.1 4.0 - - + -
30C ALA* 2.8 27.2 + - - +
43C ASP* 3.9 11.9 - - + +
46C ASP* 3.5 40.2 - - - +
47C LEU 4.4 0.7 - - - +
48C VAL* 3.2 25.9 - - + +
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Residues in contact with LYS 27 (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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25C GLU* 3.2 5.4 - - + +
26C PRO* 1.3 80.0 - - - +
28C LEU* 1.3 58.0 + - - +
30C ALA* 3.8 2.3 - - - +
31C ARG* 2.9 36.2 + - + +
43C ASP* 3.9 26.7 + - - +
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Residues in contact with LEU 28 (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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24C MET* 3.4 22.7 - - + -
25C GLU* 3.3 16.6 + - + +
27C LYS* 1.3 76.5 - - - +
29C PHE* 1.3 61.7 + - - +
31C ARG* 3.2 43.6 + - - +
32C ASN* 2.9 54.3 + - - +
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Residues in contact with PHE 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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19C PHE* 4.0 19.1 - - + -
20C TYR 4.3 0.7 - - - -
21C ASN* 3.6 45.3 - - + -
24C MET* 3.4 20.9 - - + +
25C GLU 2.9 17.4 + - - +
26C PRO* 3.6 6.3 - - + +
28C LEU* 1.3 77.5 - - - +
30C ALA* 1.3 61.0 + - - +
32C ASN* 3.3 4.1 + - + +
33C LEU* 3.0 61.4 + - + +
48C VAL* 3.7 21.8 - - + -
64C VAL* 4.9 1.1 - - + -
67C TYR* 3.7 32.3 - + + -
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Residues in contact with ALA 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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26C PRO 2.8 22.0 + - - +
27C LYS 3.8 4.0 - - - +
29C PHE* 1.3 74.1 - - - +
31C ARG* 1.3 54.2 + - - +
33C LEU* 3.4 0.8 + - - -
34C SER* 2.7 38.2 + - - -
41C PHE* 3.6 23.8 - - + +
42C GLN 4.2 0.4 - - - -
43C ASP* 4.1 14.6 - - + +
48C VAL* 3.8 25.3 - - + +
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Residues in contact with ARG 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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27C LYS* 2.9 27.3 + - + +
28C LEU* 3.2 35.1 + - - +
30C ALA* 1.3 76.2 - - - +
32C ASN* 1.3 67.4 + - - +
34C SER* 3.2 8.1 + - - -
35C ARG* 3.0 24.7 + - + +
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Residues in contact with ASN 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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24C MET* 3.6 24.9 - - - +
28C LEU* 2.9 32.4 + - - +
29C PHE* 3.8 6.3 - - + +
31C ARG* 1.3 82.7 + - - +
33C LEU* 1.3 65.3 + - + +
35C ARG* 3.2 30.8 + - - +
36C VAL* 3.2 17.5 + - + +
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Residues in contact with LEU 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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19C PHE* 4.9 4.0 - - + -
29C PHE* 3.0 57.1 + - + +
30C ALA 3.8 0.7 - - - +
32C ASN* 1.3 78.1 - - + +
34C SER* 1.3 62.5 + - - +
36C VAL* 4.0 3.1 - - + -
37C ASN* 2.8 31.5 + - - +
41C PHE* 3.4 42.9 - - + -
48C VAL* 4.1 6.3 - - + -
60C THR 4.1 13.5 - - - +
61C PRO* 4.3 8.7 - - + -
64C VAL* 4.0 25.1 - - + -
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Residues in contact with SER 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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30C ALA 2.7 19.9 + - - -
31C ARG* 3.2 8.2 + - - -
33C LEU* 1.3 76.9 - - - +
35C ARG* 1.3 58.7 + - - +
38C ASN* 3.0 26.0 + - - -
39C PHE 3.1 21.4 + - - -
40C LYS* 3.3 11.0 - - - +
41C PHE* 2.6 28.9 + - - -
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Residues in contact with ARG 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 ARG* 3.0 15.1 + - + +
32C ASN* 3.2 32.2 + - - +
34C SER* 1.3 78.9 - - - +
36C VAL* 1.3 83.4 + - - +
38C ASN* 3.6 15.4 + - - +
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Residues in contact with VAL 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 ASN* 3.2 13.2 + - + +
33C LEU* 3.6 3.6 - - + +
35C ARG* 1.3 107.5 - - - +
37C ASN* 1.3 66.5 + - - +
38C ASN* 3.5 3.5 + - - -
60C THR* 3.3 51.1 + - + +
61C PRO* 4.4 7.0 - - + -
98C ASP* 5.5 0.7 - - - +
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Residues in contact with ASN 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 LEU* 2.8 29.2 + - - +
36C VAL* 1.3 81.6 - - - +
38C ASN* 1.3 68.8 + - - +
39C PHE* 3.2 8.3 + - + +
41C PHE* 3.8 17.9 - - + -
57C PHE* 4.6 6.2 - - + -
58C GLN 4.2 2.9 - - - +
59C ILE* 3.4 16.7 - - - +
60C THR* 2.7 50.2 + - - +
94C LYS* 2.8 35.9 + - - +
98C ASP* 4.7 0.4 - - - -
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Residues in contact with ASN 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 SER 3.0 9.1 + - - -
35C ARG 3.6 10.6 + - - +
36C VAL 3.5 4.2 + - - -
37C ASN* 1.3 77.9 - - - +
39C PHE* 1.3 56.5 + - - +
90C LYS 4.6 1.2 - - - +
93C LYS* 4.7 2.8 - - - +
94C LYS* 3.3 23.1 + - - +
97C LEU* 3.7 49.5 + - + +
98C ASP* 2.9 25.2 + - - +
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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