Contacts of the helix formed by residues 35 - 43 (chain H) in PDB entry 5O9G
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 ALA 35 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33H SER* 3.1 14.5 + - - +
34H TYR* 1.3 73.0 - - - +
36H ILE* 1.3 72.2 + - + +
37H TYR* 3.2 5.0 + - - +
38H VAL 3.5 5.8 + - - -
39H TYR* 3.8 16.1 + - + -
56H MET* 3.4 24.4 - - + +
49I C 4.8 8.9 + - - +
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Residues in contact with ILE 36 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35H ALA* 1.3 79.0 - - + +
37H TYR* 1.3 77.6 + - + +
38H VAL 3.2 2.0 + - - -
39H TYR* 3.7 13.8 + - + +
40H LYS* 3.4 34.7 + - - +
48I G 3.4 48.5 - - + +
49I C 3.5 28.0 + - - +
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Residues in contact with TYR 37 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24G GLN* 3.5 16.5 - - - +
25G PHE* 3.3 33.6 - - + -
26G PRO* 3.5 45.4 - - + +
29G ARG* 4.1 22.2 + - - -
33H SER 5.3 2.2 - - - -
34H TYR* 4.4 27.1 - + + -
35H ALA 3.2 2.5 - - - -
36H ILE* 1.3 90.8 - - + +
38H VAL* 1.3 60.4 + - - +
40H LYS* 4.4 13.5 - - + -
41H VAL* 3.5 12.8 - - - +
48I G 3.1 41.6 + - - -
49I C 5.4 2.9 - - - -
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Residues in contact with VAL 38 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25G PHE* 5.1 7.9 - - + -
59G THR* 4.7 7.6 - - - +
63G LEU* 4.2 22.0 - - + -
34H TYR* 3.6 33.4 - - + +
35H ALA 3.5 0.4 + - - -
36H ILE 3.2 0.6 - - - -
37H TYR* 1.3 79.9 - - + +
39H TYR* 1.3 64.9 - - + +
40H LYS 3.3 1.8 - - - -
41H VAL* 3.3 5.5 + - - +
42H LEU* 2.9 28.9 + - + +
51H ILE* 6.4 0.4 - - + -
56H MET* 3.7 26.0 - - + -
59H MET* 5.1 15.9 - - + -
60H ASN* 6.2 1.3 - - - +
63H VAL* 6.3 2.9 - - + -
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Residues in contact with TYR 39 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35H ALA* 3.8 16.3 + - + -
36H ILE* 3.7 16.0 + - + +
38H VAL* 1.3 81.3 - - + +
40H LYS* 1.3 59.1 + - + +
42H LEU* 4.3 11.9 - - + +
43H LYS* 2.9 50.2 + - + +
51H ILE* 3.5 32.4 + - + +
56H MET* 4.7 16.4 - - + +
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Residues in contact with LYS 40 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24G GLN* 3.3 38.7 + - + +
36H ILE* 3.4 27.5 + - - +
37H TYR* 4.9 8.5 - - - +
38H VAL 3.3 0.6 - - - -
39H TYR* 1.3 78.0 - - + +
41H VAL* 1.3 59.4 + - + +
43H LYS* 4.2 4.2 + - - +
44H GLN* 3.2 31.0 + - - +
48I G 4.4 22.4 + - - -
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Residues in contact with VAL 41 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24G GLN* 3.7 25.1 - - + -
25G PHE* 4.4 11.7 - - + -
56G GLU* 4.6 18.4 - - + +
59G THR* 4.0 22.4 - - + +
60G ALA* 4.7 13.2 - - + -
63G LEU* 4.8 6.7 - - + +
37H TYR 3.5 20.2 - - - +
38H VAL* 3.3 6.2 + - - +
39H TYR 3.1 0.4 - - - -
40H LYS* 1.3 77.7 - - - +
42H LEU* 1.3 64.4 + - - +
44H GLN* 3.5 21.1 + - - +
45H VAL* 3.8 12.2 - - + +
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Residues in contact with LEU 42 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63G LEU* 3.8 43.2 - - + +
78G ILE* 5.6 6.1 - - + -
38H VAL* 2.9 19.8 + - + +
39H TYR* 3.2 12.8 + - + +
41H VAL* 1.3 76.3 - - - +
43H LYS* 1.3 65.2 + - + +
44H GLN 3.2 0.3 + - - -
45H VAL* 3.3 6.8 + - + +
46H HIS* 2.8 45.2 + - + +
49H THR* 4.3 23.8 - - - +
50H GLY 4.5 13.5 - - - +
51H ILE* 4.5 18.8 - - + -
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Residues in contact with LYS 43 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39H TYR* 2.9 33.9 + - + +
40H LYS* 4.7 4.9 - - - +
41H VAL 3.4 0.2 - - - -
42H LEU* 1.3 81.9 - - + +
44H GLN* 1.3 60.8 + - + +
45H VAL 3.3 1.2 + - - -
46H HIS 3.8 6.0 + - - +
47H PRO* 3.4 49.1 + - + +
48H ASP* 5.0 0.8 - - - +
49H THR 3.7 22.2 + - - +
-54J C 6.1 3.2 - - - -
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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
------------------------------------------------------------
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