Contacts of the helix formed by residues 32 - 47 (chain C) in PDB entry 7BRU
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 PRO 32 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30C GLU 4.2 4.9 - - - +
31C HIS* 1.3 89.5 - - + +
33C PHE* 1.3 67.2 + - - +
34C GLU* 3.3 6.1 - - + +
35C LYS* 3.4 18.4 + - + +
36C ARG* 3.1 20.7 + - - +
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Residues in contact with PHE 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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32C PRO* 1.3 73.6 - - - +
34C GLU* 1.3 59.3 + - - +
36C ARG* 3.3 26.5 + - - +
37C ARG* 2.9 29.3 + - - +
124C ASP* 4.7 1.7 - - - +
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Residues in contact with GLU 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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32C PRO* 3.3 4.1 - - + +
33C PHE* 1.3 77.2 - - - +
35C LYS* 1.3 59.9 + - - +
37C ARG* 3.3 6.0 + - - +
38C SER* 3.0 30.0 + - - -
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Residues in contact with LYS 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 HIS* 5.5 2.5 - - + -
32C PRO* 3.4 28.5 + - + +
34C GLU* 1.3 77.4 - - - +
36C ARG* 1.3 59.6 + - + +
38C SER* 3.9 4.8 - - - -
39C GLU* 2.9 31.3 + - - +
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Residues in contact with ARG 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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27C TYR* 3.8 22.9 - - + +
28C LYS* 3.3 18.5 + - - +
31C HIS* 2.6 53.6 + - + -
32C PRO 3.1 24.3 + - - +
33C PHE* 3.3 19.2 - - - +
35C LYS* 1.3 74.1 - - - +
37C ARG* 1.3 60.5 + - - +
39C GLU* 4.4 4.5 - - - +
40C GLY 2.8 24.6 + - - -
124C ASP* 3.1 42.4 + - + +
126C PHE* 3.2 11.6 - - + -
128C TYR* 3.2 16.3 + - - -
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Residues in contact with ARG 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 PHE 2.9 18.7 + - - +
34C GLU* 3.3 7.4 + - - +
36C ARG* 1.3 78.1 - - - +
38C SER* 1.3 55.7 + - - +
40C GLY* 4.1 0.2 - - - -
41C GLU* 3.0 43.2 + - - +
123C GLU 4.6 4.9 - - - +
124C ASP* 3.8 21.5 - - + +
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Residues in contact with SER 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 GLU 3.0 17.2 + - - -
35C LYS* 3.9 4.9 - - - -
37C ARG* 1.3 74.1 - - - +
39C GLU* 1.3 59.8 + - - +
41C GLU* 3.4 12.1 + - - +
42C LYS* 2.9 32.7 + - - +
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Residues in contact with GLU 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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5B PRO* 5.7 1.4 - - - +
6B PHE* 3.9 15.2 - - + -
27C TYR* 3.0 21.4 + - - -
31C HIS* 5.6 1.2 - - - -
35C LYS 2.9 18.4 + - - +
36C ARG* 4.0 7.1 - - - +
38C SER* 1.3 76.6 - - - +
40C GLY* 1.3 62.2 + - - +
42C LYS* 3.3 5.4 + - - +
43C ILE* 3.0 24.8 + - + +
70C LYS* 3.7 21.0 + - - -
126C PHE* 3.6 16.5 - - + -
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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 ARG 2.8 17.5 + - - -
39C GLU* 1.3 73.7 - - - +
41C GLU* 1.3 56.4 + - - +
43C ILE* 4.0 2.3 - - - +
44C ARG* 2.9 32.1 + - - +
52C PRO* 4.5 5.4 - - - +
124C ASP 3.6 6.1 - - - -
125C PHE* 3.8 13.3 - - - +
126C PHE* 3.5 23.9 - - - -
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Residues in contact with GLU 41 (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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37C ARG* 3.0 30.5 + - - +
38C SER* 3.7 11.4 + - - +
40C GLY* 1.3 73.5 - - - +
42C LYS* 1.3 54.7 + - - +
44C ARG* 3.6 4.2 - - - +
45C LYS* 2.7 39.0 + - - +
124C ASP 5.9 0.4 - - - -
125C PHE* 4.0 10.3 - - + +
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Residues in contact with LYS 42 (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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38C SER* 2.9 19.2 + - - +
39C GLU* 3.3 6.9 + - - +
41C GLU* 1.3 75.5 - - - +
43C ILE* 1.3 58.0 + - - +
45C LYS* 3.8 4.4 - - - +
46C LYS* 2.8 32.7 + - - +
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Residues in contact with ILE 43 (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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6B PHE* 4.6 21.1 - - + -
39C GLU* 3.0 16.3 + - + +
40C GLY* 4.3 3.4 - - - +
42C LYS* 1.3 77.2 - - - +
44C ARG* 1.3 54.0 + - - +
46C LYS* 4.3 4.7 - - - -
47C TYR* 2.7 43.3 + - + +
52C PRO* 5.2 3.1 - - + -
72C LEU* 4.7 20.2 - - + -
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Residues in contact with ARG 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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40C GLY 2.9 21.9 + - - +
41C GLU* 3.8 4.7 - - - +
43C ILE* 1.3 77.4 - - - +
45C LYS* 1.3 60.8 + - - +
47C TYR 4.4 4.7 - - - -
48C PRO* 3.7 22.7 - - - +
50C ARG 5.2 1.8 - - - +
52C PRO* 4.9 11.6 - - + +
117C TYR* 4.2 19.7 - - + +
125C PHE* 4.7 2.5 - - + -
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Residues in contact with LYS 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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41C GLU* 2.7 22.2 + - + +
42C LYS* 4.0 3.6 - - - +
44C ARG* 1.3 74.2 - - - +
46C LYS* 1.3 62.7 + - - +
47C TYR 3.6 0.2 + - - -
48C PRO* 3.9 8.8 - - - +
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Residues in contact with LYS 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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42C LYS 2.8 23.7 + - - +
43C ILE* 3.9 3.8 - - - +
45C LYS* 1.3 73.5 - - - +
47C TYR* 1.3 75.6 + - + +
48C PRO* 3.4 7.8 - - - +
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Residues in contact with TYR 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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8B VAL* 6.6 0.2 - - + -
43C ILE* 2.7 23.6 + - + +
44C ARG* 3.7 5.3 - - - +
46C LYS* 1.3 88.0 - - + +
48C PRO* 1.3 62.2 - - - +
49C ASP* 3.2 5.7 + - + -
50C ARG* 2.7 46.6 + - + +
72C LEU* 3.8 28.3 - - + -
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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