Contacts of the helix formed by residues 38 - 46 (chain C) in PDB entry 4U2M
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 HIS 38 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C LEU* 3.7 22.9 - - - -
17C GLN* 3.1 17.2 + - + -
18C ARG* 3.9 7.9 - - - -
22C LEU 3.1 18.2 + - - -
23C LEU 3.4 19.7 - - - -
24C CYS* 3.9 8.5 - - - -
25C ASP* 3.3 6.3 - - - +
26C CYS* 4.7 1.3 - - - -
37C ALA* 1.3 74.3 - - - +
39C LYS* 1.3 65.8 + - - +
40C ALA* 4.3 4.3 - - + +
41C VAL* 3.8 16.1 - - + +
42C LEU* 3.1 22.2 + - - +
78C TYR* 2.6 34.6 + + - +
171C THR* 2.9 33.4 - - + +
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Residues in contact with LYS 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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25C ASP* 2.8 48.0 + - - +
26C CYS* 4.0 7.6 - - + +
37C ALA 4.1 0.4 + - - -
38C HIS* 1.3 72.0 - - - +
40C ALA* 1.3 58.3 + - - +
42C LEU* 3.3 2.8 + - - +
43C ALA* 2.8 31.7 + - - +
53C PHE* 3.8 56.8 + - + +
154C LEU* 4.3 21.0 - - + +
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Residues in contact with ALA 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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25C ASP* 5.0 1.4 + - - -
38C HIS* 3.2 5.2 - - + +
39C LYS* 1.3 81.8 - - - +
41C VAL* 1.3 57.5 + - + +
43C ALA* 3.5 0.6 + - - -
44C ALA* 2.9 29.1 + - - +
145C LEU* 3.6 12.9 - - + +
148C LEU* 3.6 6.9 - - + +
154C LEU* 4.2 16.1 - - + +
169C HIS* 3.7 35.2 - - + +
171C THR* 6.1 3.6 - - - -
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Residues in contact with VAL 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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11C LEU* 5.8 0.9 - - + -
14C LEU* 3.9 32.5 - - + -
38C HIS* 3.1 22.6 + - + +
40C ALA* 1.3 79.1 - - + +
42C LEU* 1.3 64.9 + - + +
44C ALA* 3.1 7.8 + - - +
45C CYS* 3.1 34.4 + - - -
77C MET* 4.8 5.8 - - + +
78C TYR* 3.7 40.6 - - + +
141C VAL* 5.0 6.1 - - + -
145C LEU* 4.5 8.5 - - + -
171C THR* 4.9 1.8 - - + -
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Residues in contact with LEU 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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26C CYS* 4.2 2.9 - - - -
28C PHE* 3.6 37.5 - - + -
37C ALA* 3.8 21.3 - - + -
38C HIS 3.1 14.4 + - - +
39C LYS 3.6 6.3 - - - +
41C VAL* 1.3 77.4 - - - +
43C ALA* 1.3 58.3 + - - +
45C CYS* 3.1 3.1 + - - +
46C SER* 2.9 32.4 + - - -
49C PHE* 3.8 28.3 - - + -
53C PHE* 3.9 14.6 - - + -
74C LEU* 3.9 9.0 - - + -
77C MET* 3.6 23.8 - - - -
78C TYR* 4.3 8.7 - - + -
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Residues in contact with ALA 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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39C LYS 2.8 20.6 + - - +
40C ALA 3.8 3.1 - - - +
42C LEU* 1.3 73.4 - - - +
44C ALA* 1.3 60.6 + - - +
45C CYS 3.4 0.7 + - - -
46C SER 3.5 13.2 + - - +
47C GLU* 5.2 0.2 - - - -
49C PHE* 4.1 1.9 - - - +
50C LYS* 3.7 44.1 - - + +
148C LEU* 4.0 10.4 - - + +
154C LEU* 3.6 24.2 - - + -
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Residues in contact with ALA 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 ALA 2.9 18.3 + - - +
41C VAL* 3.1 7.4 + - - +
43C ALA* 1.3 75.8 - - - +
45C CYS* 1.3 60.8 + - - +
141C VAL* 4.0 21.9 - - + +
144C ASN* 3.0 46.9 + - + +
145C LEU* 4.0 15.0 - - + +
148C LEU* 4.1 5.1 - - + +
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Residues in contact with CYS 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 VAL* 3.1 19.7 + - - +
42C LEU 3.1 5.1 + - - +
44C ALA* 1.3 79.8 - - - +
46C SER* 1.3 57.3 + - - +
76C PHE* 5.6 0.2 - - + -
77C MET* 3.8 41.3 - - + -
101C MET* 3.9 19.3 - - + +
137C HIS* 3.8 13.2 - - + -
141C VAL* 3.7 28.7 - - - -
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Residues in contact with SER 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 LEU 2.9 13.5 + - - +
43C ALA 3.5 11.7 + - - +
45C CYS* 1.3 80.0 - - - +
47C GLU* 1.3 64.0 + - - +
48C TYR* 3.3 3.5 + - - +
49C PHE* 3.2 28.6 + - - -
50C LYS 3.0 18.2 + - - -
77C MET* 4.3 4.7 - - - -
99C LEU* 2.9 28.0 + - - +
100C GLN 5.7 0.7 - - - -
101C MET* 4.3 9.9 - - - -
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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