Contacts of the helix formed by residues 28 - 37 (chain C) in PDB entry 4M3P
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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27C GLY* 1.3 68.1 - - - -
29C PHE* 1.3 60.4 + - - -
30C VAL 3.6 1.8 - - - -
31C PHE* 3.7 3.9 + - - +
32C ALA* 3.0 33.5 + - - +
63C PHE* 3.9 1.9 - - - -
299C CYS 3.4 25.9 + - - -
300C CYS* 4.1 4.7 - - - -
301C GLY 4.7 1.0 + - - -
302C PHE 3.2 14.8 + - - +
503C HCS 3.6 7.6 - - - -
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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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26C ASP* 3.6 18.2 - - - -
27C GLY 4.1 4.3 - - - -
28C GLY* 1.3 71.5 - - - +
30C VAL* 1.3 59.8 + - - +
32C ALA* 3.9 0.2 - - - -
33C LEU* 2.9 43.1 + - + +
56C VAL* 4.1 8.3 - - + -
59C LEU* 3.7 27.6 - - + -
60C HIS* 3.2 52.7 - + - -
63C PHE* 3.4 27.8 - + - -
72C GLN* 5.2 3.8 - - + -
74C PHE* 3.7 34.8 - + + -
503C HCS 2.7 22.5 + - - +
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Residues in contact with VAL 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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29C PHE* 1.3 72.5 - - - +
31C PHE* 1.3 74.3 + - + +
34C GLU* 3.0 25.5 + - - +
39C VAL* 3.9 12.4 - - + +
44C TRP* 3.8 47.9 - - + +
45C THR 5.7 0.2 - - - -
46C PRO* 5.8 0.4 - - + -
74C PHE* 3.7 23.6 - - + -
300C CYS* 4.5 3.6 - - - -
503C HCS 2.9 38.9 + - + +
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Residues in contact with PHE 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C GLY 3.7 2.5 + - - +
29C PHE 3.3 0.6 - - - -
30C VAL* 1.3 84.2 - - + +
32C ALA* 1.3 65.0 + - - +
34C GLU* 3.5 6.7 + - - +
35C LYS* 3.2 33.2 + - + +
44C TRP* 3.5 34.5 - + - -
251C TYR* 3.2 34.5 - + - -
261C PHE* 4.1 9.6 - + - -
267C PHE* 4.0 24.7 - + - -
268C PRO* 4.2 11.4 - - + -
271C LEU* 3.9 16.4 - - + -
300C CYS* 3.7 28.0 - - + -
301C GLY* 3.9 17.3 - - - +
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Residues in contact with ALA 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 3.0 21.0 + - - +
31C PHE* 1.3 76.6 - - - +
33C LEU* 1.3 63.3 + - - +
35C LYS* 3.3 6.0 + - - +
36C ARG* 3.2 29.1 + - - +
59C LEU* 3.9 23.6 - - + -
63C PHE* 5.3 1.1 - - + -
302C PHE 4.8 4.5 - - - +
303C GLU* 3.4 32.4 - - - +
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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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29C PHE* 2.9 33.3 + - + +
32C ALA* 1.3 74.8 - - - +
34C GLU* 1.3 58.6 + - - +
36C ARG* 3.2 13.6 + - - +
37C GLY 2.9 11.1 + - - -
38C TYR* 2.9 46.2 + - + +
39C VAL* 3.6 15.0 - - + -
48C ALA* 5.0 2.5 - - + -
55C ALA* 4.1 21.1 - - + +
56C VAL* 4.3 13.2 - - + -
59C LEU* 3.7 17.3 - - + -
74C PHE* 3.7 32.1 - - + -
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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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30C VAL 3.0 19.7 + - - +
31C PHE* 3.6 5.1 - - - +
33C LEU* 1.3 74.5 - - - +
35C LYS* 1.3 68.4 + - - +
37C GLY* 3.3 13.0 + - - -
39C VAL* 3.4 26.5 - - + +
41C ALA* 3.9 20.4 + - + +
44C TRP* 4.0 16.6 - - + -
269C PHE* 4.2 2.7 - - - -
278D ARG* 2.9 44.8 + - - -
308D ARG* 3.4 21.0 + - - -
327D LYS 4.6 1.0 - - - +
328D HIS* 4.0 6.4 - - - -
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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 PHE* 3.2 22.9 + - + +
32C ALA 3.7 5.6 - - - +
33C LEU 3.3 0.2 - - - -
34C GLU* 1.3 89.3 - - - +
36C ARG* 1.3 60.6 + - + +
251C TYR* 4.6 14.4 + - - +
272C GLU* 5.4 2.0 - - - +
275C VAL* 5.6 6.7 - - - +
301C GLY* 5.1 5.8 + - - -
303C GLU* 3.6 31.8 + - - +
278D ARG* 4.4 3.4 - - - +
303D GLU* 5.7 2.9 - - + +
304D PRO* 3.6 4.5 - - - +
305D TYR* 3.0 69.8 + - + +
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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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32C ALA* 3.2 18.2 + - - +
33C LEU* 3.2 17.8 + - - +
35C LYS* 1.3 78.4 - - + +
37C GLY* 1.3 57.3 + - - +
38C TYR* 3.4 21.5 - - + -
55C ALA 5.5 1.4 + - - -
58C GLN* 5.2 2.4 - - - +
59C LEU* 3.6 26.8 - - - +
62C GLU* 2.8 38.2 + - - -
303C GLU* 2.9 28.9 + - - -
304C PRO* 4.0 1.4 - - - +
36D ARG* 3.6 34.0 - - - +
62D GLU* 3.5 43.4 + - - +
65D ARG* 4.9 1.7 - - - +
303D GLU* 5.5 0.7 - - - +
304D PRO* 4.0 14.7 - - + +
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Residues in contact with GLY 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 2.9 2.8 + - - -
34C GLU 3.3 10.3 + - - -
35C LYS 3.3 0.8 - - - -
36C ARG* 1.3 77.2 - - - +
38C TYR* 1.3 64.1 + - - +
39C VAL 3.7 1.6 - - - -
65D ARG* 2.9 32.6 + - - -
308D ARG* 4.0 14.1 - - - -
324D ALA* 4.3 10.9 - - - -
327D LYS* 3.5 10.2 - - - +
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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