Contacts of the helix formed by residues 15 - 26 (chain C) in PDB entry 1MN8
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 15 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11C LEU* 3.0 39.1 + - + +
12C THR 3.4 3.6 - - - -
13C LEU 3.2 0.2 - - - -
14C GLY* 1.3 84.1 + - - +
16C TRP* 1.3 63.4 + - - +
17C LYS 3.3 2.2 - - - -
18C ASP* 3.1 19.6 + - - +
19C VAL* 3.1 12.0 + - - +
96C TRP* 3.3 65.3 - + + +
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Residues in contact with TRP 16 (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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12C THR 3.3 18.1 + - - -
13C LEU* 3.6 16.4 + - + +
14C GLY 3.6 1.8 - - - -
15C HIS* 1.3 77.0 - - - +
17C LYS* 1.3 71.8 + - + +
19C VAL* 3.0 15.5 + - + +
20C GLU* 2.9 59.6 + - + +
30C VAL* 3.7 28.2 + - + -
31C LYS 3.7 4.5 - - - -
32C LYS* 3.4 60.5 - - + +
35C TRP* 3.6 52.5 - + + -
17D LYS* 5.3 0.7 - - - -
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Residues in contact with LYS 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C HIS 3.3 0.8 - - - -
16C TRP* 1.3 84.1 - - + +
18C ASP* 1.3 63.1 + - - +
20C GLU* 3.0 20.8 + - - +
21C ARG* 3.1 30.3 + - - +
16D TRP* 5.1 1.6 - - - +
17D LYS* 2.9 24.4 - - - +
20D GLU* 2.7 29.8 + - - -
24D HIS* 5.3 0.2 + - - -
31D LYS* 4.7 22.0 - - - +
32D LYS* 5.4 5.3 - - - +
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Residues in contact with ASP 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C HIS* 3.1 16.7 + - - +
17C LYS* 1.3 76.9 - - - +
19C VAL* 1.3 65.5 + - - +
21C ARG* 3.2 21.3 + - - +
22C ILE* 3.0 34.2 + - + +
94C PRO* 5.1 1.7 - - + +
95C PRO* 5.8 0.7 - - - +
96C TRP* 2.8 35.5 + - + +
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Residues in contact with VAL 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C THR* 3.7 23.8 - - - +
15C HIS 3.5 12.1 - - - +
16C TRP* 3.0 33.3 + - + +
18C ASP* 1.3 77.3 - - - +
20C GLU* 1.3 58.0 + - - +
22C ILE* 3.2 9.5 + - - +
23C ALA* 2.9 27.5 + - - +
30C VAL* 4.3 2.7 - - + -
35C TRP* 3.8 11.7 - - + -
85C THR* 3.8 21.4 - - + +
89C LEU* 4.5 6.3 - - + -
96C TRP* 3.8 20.9 - - + -
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Residues in contact with GLU 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C TRP* 2.9 48.9 + - + +
17C LYS* 3.0 37.7 - - - +
19C VAL* 1.3 76.4 - - - +
21C ARG* 1.4 57.2 + - - +
23C ALA* 3.3 7.1 + - - +
24C HIS* 2.9 50.0 + - + +
29C ASP* 5.7 1.2 - - - +
30C VAL* 4.4 13.7 - - + +
17D LYS* 2.7 31.5 + - - -
20D GLU* 4.1 2.9 - - - +
24D HIS* 5.2 4.2 + - - +
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Residues in contact with ARG 21 (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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17C LYS* 3.1 21.1 + - - +
18C ASP* 3.2 19.6 + - - +
20C GLU* 1.4 76.5 - - - +
22C ILE* 1.3 59.2 + - + +
24C HIS* 3.3 1.9 + - - +
25C ASN* 3.0 29.6 + - - +
24D HIS* 3.6 37.5 + - + +
29D ASP* 4.3 24.7 + - - +
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Residues in contact with ILE 22 (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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18C ASP* 3.0 29.7 + - + +
19C VAL* 3.5 5.4 - - - +
21C ARG* 1.3 77.9 - - + +
23C ALA* 1.3 61.3 + - - +
25C ASN* 3.3 8.9 + - - +
26C GLN* 3.3 23.2 + - - +
85C THR* 4.4 7.6 - - + -
88C ALA* 3.9 26.0 - - + -
89C LEU* 3.6 32.8 - - + +
92C ASP 5.6 2.0 - - - +
94C PRO* 4.1 17.9 - - + -
96C TRP* 5.0 0.2 - - + -
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Residues in contact with ALA 23 (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 VAL 2.9 13.5 + - - +
20C GLU* 3.5 8.5 - - - +
22C ILE* 1.3 73.2 - - - +
24C HIS* 1.3 65.7 + - - +
26C GLN* 2.9 15.1 + - - -
28C VAL* 3.0 34.0 + - + +
29C ASP* 4.5 0.7 - - - -
30C VAL* 3.9 20.0 - - + +
85C THR* 3.3 27.6 - - - +
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Residues in contact with HIS 24 (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 GLU* 2.9 30.2 + - + +
21C ARG 3.3 5.1 + - - +
23C ALA* 1.3 75.4 - - - +
25C ASN* 1.3 57.3 + - - +
27C SER* 2.9 20.5 + - - +
28C VAL 3.3 16.3 + - - -
29C ASP* 2.7 32.8 - - + +
30C VAL 5.3 0.7 - - - -
20D GLU* 5.3 2.8 + - - +
21D ARG* 3.6 30.7 + - + +
24D HIS* 2.7 49.7 + + + -
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Residues in contact with ASN 25 (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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21C ARG 3.0 16.8 + - - +
22C ILE* 3.6 8.0 + - - +
23C ALA 3.1 0.4 - - - -
24C HIS* 1.3 78.5 - - - +
26C GLN* 1.3 71.6 + - - +
27C SER* 3.2 4.0 + - - -
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Residues in contact with GLN 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C ILE* 3.3 13.0 + - - +
23C ALA* 2.9 10.0 + - - +
25C ASN* 1.3 96.4 + - - +
27C SER* 1.3 69.6 + - - +
28C VAL* 3.2 10.0 + - + +
84C VAL* 3.8 26.2 - - + +
85C THR* 5.5 0.7 - - - -
88C ALA* 4.0 26.6 - - + +
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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