Contacts of the helix formed by residues 29 - 39 (chain C) in PDB entry 6CM9
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 29 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27C ALA 3.5 2.2 - - - -
28C ALA* 1.3 72.5 - - - +
30C LYS* 1.3 58.4 + - - -
31C THR 3.6 1.6 - - - -
32C THR* 3.4 5.4 - - - -
33C ILE* 3.3 22.0 + - - +
126C ASN* 2.9 13.1 + - - +
160C ALA* 4.7 0.2 - - - +
1001C GTP 2.5 54.7 + - - -
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Residues in contact with LYS 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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22C MET* 3.3 31.6 - - + +
23C VAL 4.4 12.1 - - - +
24C GLY 4.0 9.9 - - - -
25C LEU 3.4 23.0 + - - +
26C ASP* 3.4 2.0 - - - +
28C ALA* 4.5 1.5 - - + +
29C GLY* 1.3 73.8 - - - +
31C THR* 1.3 63.0 + - - +
32C THR 3.2 1.1 - - - -
33C ILE* 3.3 7.0 - - - +
34C LEU* 2.9 26.9 + - - +
67C ASP* 3.3 23.1 - - - +
68C VAL 3.6 17.0 - - - -
69C GLY* 4.1 0.9 - - - -
91C VAL* 4.0 16.4 - - + -
126C ASN* 4.0 1.3 - - - +
1001C GTP 2.7 47.6 + - - +
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Residues in contact with THR 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C LYS* 1.3 75.1 - - - +
32C THR* 1.3 57.0 + - - +
34C LEU* 3.7 7.2 - - + -
35C TYR* 3.0 41.6 + - + +
43C VAL* 4.2 2.4 - - - +
45C THR* 4.1 9.9 - - + +
48C THR* 3.7 3.2 - - + +
52C ASN* 3.3 20.6 - - + +
67C ASP* 3.3 26.0 - - + +
1001C GTP 2.5 26.6 + - - -
1002C MG 2.4 35.2 - - - -
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Residues in contact with THR 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C GLY* 3.4 16.1 - - - -
30C LYS 3.2 0.2 - - - -
31C THR* 1.3 77.0 - - - +
33C ILE* 1.3 57.4 + - - +
35C TYR* 3.4 2.3 + - - +
36C LYS* 2.9 25.9 + - + +
41C GLU 4.3 4.0 - - - +
42C ILE* 4.4 30.7 - - + -
43C VAL* 4.6 14.8 + - - +
45C THR* 6.5 0.2 - - - -
160C ALA* 3.9 22.9 - - + +
161C THR* 6.4 0.4 - - + -
1001C GTP 3.1 36.3 + - + +
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Residues in contact with ILE 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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22C MET* 3.7 18.4 - - + -
29C GLY 3.3 6.7 - - - +
30C LYS* 3.3 14.4 - - - +
32C THR* 1.3 75.0 - - - +
34C LEU* 1.3 59.5 + - - +
36C LYS* 3.5 7.2 - - + +
37C LEU* 2.9 36.0 + - + +
91C VAL* 4.8 2.5 - - + -
124C PHE* 4.3 18.4 - - + -
126C ASN* 3.5 26.0 - - + +
158C THR* 4.5 3.1 - - - +
159C CYS 5.0 0.7 - - - -
160C ALA* 3.7 35.7 - - + +
166C LEU* 4.0 30.3 - - + -
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Residues in contact with LEU 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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22C MET* 3.9 10.3 - - - -
30C LYS 2.9 17.2 + - - +
31C THR* 3.4 8.1 - - + +
32C THR 3.2 0.4 - - - -
33C ILE* 1.3 76.7 - - - +
35C TYR* 1.3 92.4 + - + +
37C LEU* 3.3 8.6 + - - +
38C LYS* 2.9 28.9 + - + +
52C ASN* 4.8 9.9 - - + +
54C GLU* 5.6 10.8 - - + +
56C VAL* 5.3 1.0 - - - +
65C VAL* 3.7 33.4 - - + +
67C ASP* 3.6 33.2 - - + +
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Residues in contact with TYR 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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93B LYS* 3.3 42.6 + - + +
31C THR* 3.0 33.7 + - - -
32C THR 3.8 0.2 - - - -
34C LEU* 1.3 91.9 - - + +
36C LYS* 1.3 59.2 + - - +
38C LYS* 3.6 24.0 - - + -
39C LEU* 2.7 38.9 + - + +
40C GLY 3.1 6.1 + - - -
41C GLU 4.0 4.2 + - - -
43C VAL* 3.7 38.1 - - + -
45C THR* 5.1 2.0 - - - -
52C ASN* 3.8 12.4 + - - +
54C GLU* 4.8 15.5 + - + +
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Residues in contact with LYS 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 THR 2.9 17.4 + - - +
33C ILE* 3.5 11.4 - - - +
34C LEU 3.2 0.4 - - - -
35C TYR* 1.3 76.8 - - - +
37C LEU* 1.3 62.3 + - - +
39C LEU 3.9 0.3 - - - -
40C GLY* 3.2 47.1 + - - +
41C GLU* 3.9 12.8 + - - +
42C ILE* 4.8 4.7 - - + +
160C ALA 4.7 11.4 - - - +
161C THR 5.4 2.0 + - - -
162C SER 3.6 25.3 + - - -
163C GLY* 4.0 8.7 - - - -
166C LEU* 3.8 20.2 - - + -
167C TYR* 4.2 6.7 + - + -
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Residues in contact with LEU 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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22C MET* 5.9 5.6 - - + -
33C ILE* 2.9 23.6 + - + +
34C LEU* 3.7 6.1 - - - +
36C LYS* 1.3 75.9 - - - +
38C LYS* 1.3 64.8 + - - +
39C LEU 5.1 0.5 - - - -
56C VAL* 4.0 26.6 - - + +
65C VAL* 5.9 6.7 - - + -
124C PHE* 5.7 6.5 - - + -
166C LEU* 3.7 36.8 - - + -
167C TYR* 3.6 41.8 + - + +
170C LEU* 3.8 28.7 - - + -
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Residues in contact with LYS 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C LEU* 2.9 19.8 + - + +
35C TYR* 3.7 25.6 - - + -
37C LEU* 1.3 81.3 - - - +
39C LEU* 1.3 78.3 + - + +
54C GLU* 3.7 33.0 - - + -
55C THR* 3.3 27.6 - - - +
56C VAL* 4.3 8.0 - - + +
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Residues in contact with LEU 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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35C TYR* 2.7 23.7 + - + +
36C LYS 3.9 1.6 - - - -
37C LEU 5.0 0.4 - - - -
38C LYS* 1.3 98.5 - - + +
40C GLY* 1.3 57.5 + - - +
41C GLU* 4.3 13.7 - - + +
43C VAL* 4.7 18.4 - - + -
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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