Contacts of the helix formed by residues 29 - 38 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27H ALA 3.4 2.0 - - - -
28H ALA* 1.3 74.5 - - - +
30H LYS* 1.3 57.1 + - - -
31H THR 3.4 2.5 - - - -
32H THR* 3.2 3.2 + - - -
33H ILE* 2.8 31.9 + - - +
126H ASN* 3.5 4.1 + - - -
1001H GTP 2.6 52.7 + - - -
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Residues in contact with LYS 30 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22H MET* 3.4 37.7 - - + +
23H VAL 3.3 3.2 - - - -
24H GLY* 2.9 46.4 + - - +
25H LEU 3.6 11.5 + - - -
28H ALA* 3.3 7.7 - - - -
29H GLY* 1.3 75.8 - - - +
31H THR* 1.3 63.7 + - - +
33H ILE* 3.4 2.9 + - - -
34H LEU* 2.9 27.9 + - - +
67H ASP* 3.4 11.8 - - - +
68H VAL 3.1 29.2 + - - +
69H GLY* 4.2 0.6 - - - -
70H GLY 4.0 3.8 - - - +
78H TRP* 4.6 0.2 - - - -
91H VAL* 4.7 7.6 - - + -
1001H GTP 3.3 28.1 + - - +
1002H MG 4.4 0.4 - - - -
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Residues in contact with THR 31 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30H LYS* 1.3 72.7 - - + +
32H THR* 1.3 59.9 + - - +
34H LEU* 4.1 4.5 - - - -
35H TYR* 2.9 41.3 + - - +
45H THR* 3.3 22.6 + - - +
48H THR* 3.3 16.2 - - + +
52H ASN* 3.7 4.5 - - - +
67H ASP* 3.2 27.6 - - - +
1001H GTP 2.6 22.6 + - - +
1002H MG 2.0 35.3 - - - -
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Residues in contact with THR 32 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29H GLY* 3.2 13.0 + - - -
31H THR* 1.3 75.0 + - - +
33H ILE* 1.3 58.4 + - - +
35H TYR* 3.7 2.4 - - - +
36H LYS* 2.9 31.8 + - - +
41H GLU 5.1 0.3 - - - +
42H ILE* 3.7 40.5 - - + +
43H VAL* 5.3 4.1 + - - +
45H THR* 5.1 4.5 + - - -
160H ALA* 3.8 15.7 - - + -
161H THR* 4.1 2.7 - - + -
1001H GTP 2.8 39.9 + - + +
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Residues in contact with ILE 33 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22H MET* 3.7 15.9 - - + -
29H GLY 2.8 15.0 + - - +
30H LYS 3.6 6.7 - - - +
31H THR 3.3 0.2 - - - -
32H THR* 1.3 75.5 - - - +
34H LEU* 1.3 59.0 + - - +
36H LYS* 3.7 4.6 - - - -
37H LEU* 2.9 45.2 + - + +
89H ILE* 6.1 0.2 - - + -
91H VAL* 3.9 17.3 - - + -
124H PHE* 3.7 27.8 - - + -
126H ASN* 3.4 28.7 - - + +
158H THR* 4.5 0.7 - - - +
160H ALA* 3.7 11.7 - - + -
166H LEU* 3.7 25.1 - - + -
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Residues in contact with LEU 34 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22H MET* 4.4 3.8 - - - -
30H LYS 2.9 17.3 + - - +
31H THR* 3.2 7.1 + - - +
33H ILE* 1.3 78.9 - - - +
35H TYR* 1.3 68.8 + - + +
37H LEU* 4.6 2.9 - - + -
38H LYS* 3.5 21.5 + - - +
52H ASN* 4.1 21.5 - - + -
53H VAL 4.8 0.2 - - - -
54H GLU* 3.6 37.0 - - + +
56H VAL* 4.8 6.1 - - + -
65H VAL* 3.7 36.8 - - + +
67H ASP* 3.7 17.9 - - + -
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Residues in contact with TYR 35 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109G ASN* 5.0 7.3 + - - -
31H THR* 2.9 33.1 + - - +
32H THR* 3.7 3.1 - - - +
34H LEU* 1.3 90.9 - - + +
36H LYS* 1.3 59.6 + - - +
37H LEU 3.6 0.2 - - - -
38H LYS* 5.3 0.4 - - + -
39H LEU* 3.6 34.0 - - + +
40H GLY 3.1 15.9 + - - -
41H GLU 3.1 15.1 - - - +
43H VAL* 3.7 31.4 - - + -
45H THR* 4.8 8.1 - - + -
52H ASN* 3.4 30.6 + - - +
54H GLU* 3.9 29.5 + - + -
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Residues in contact with LYS 36 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32H THR 2.9 18.8 + - - +
33H ILE 3.2 3.1 + - - +
35H TYR* 1.3 79.2 - - - +
37H LEU* 1.3 63.3 + - - +
38H LYS 3.5 0.2 - - - -
39H LEU 4.3 0.2 - - - -
40H GLY* 3.3 40.7 + - - +
41H GLU* 4.3 4.8 + - - +
42H ILE* 3.7 22.4 - - + +
160H ALA 3.5 15.0 - - - +
161H THR 5.1 1.0 + - - -
162H SER* 4.0 8.4 + - - +
163H GLY* 3.6 26.7 - - - +
166H LEU* 3.8 19.3 - - + -
167H TYR* 3.4 16.0 + - + +
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Residues in contact with LEU 37 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22H MET* 5.8 2.5 - - - -
33H ILE* 2.9 38.4 + - + +
34H LEU* 4.6 3.4 - - + +
36H LYS* 1.3 78.4 - - - +
38H LYS* 1.3 63.0 + - - +
56H VAL* 4.0 28.1 - - + +
65H VAL* 6.1 3.8 - - + -
89H ILE* 5.8 2.9 - - + -
124H PHE* 5.3 3.1 - - + -
166H LEU* 3.7 31.9 - - + +
167H TYR* 3.9 32.3 + - + -
170H LEU* 3.7 37.2 - - + -
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Residues in contact with LYS 38 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34H LEU 3.5 18.2 + - - +
35H TYR* 4.8 0.7 - - - -
37H LEU* 1.3 82.2 - - - +
39H LEU* 1.3 83.7 + - + +
54H GLU* 3.6 37.3 + - + +
55H THR* 3.3 36.8 - - - +
56H VAL* 4.2 8.3 - - + -
57H GLU 5.4 0.7 - - - +
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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