Contacts of the strand formed by residues 46 - 53 (chain E) in PDB entry 5HHM
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 ARG 46 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37E TYR* 3.1 6.9 - - - -
38E ARG* 3.0 63.7 + - + +
40E ASP* 3.2 26.9 + - - -
43E GLN* 5.1 7.6 - - - +
44E GLY 5.0 3.1 - - - +
45E LEU* 1.3 77.7 - - - +
47E LEU* 1.3 63.2 + - - +
48E ILE* 3.4 1.9 + - - +
61E ASP* 6.1 3.1 - - + -
62E ILE* 3.4 45.4 - - + +
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Residues in contact with LEU 47 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98D ASN* 3.5 32.8 - - + +
99D LEU 5.5 2.7 - - - +
35E TYR* 4.1 18.2 - - + -
36E TRP 3.3 17.7 - - - +
37E TYR* 3.8 27.4 - - + +
45E LEU 4.3 0.4 - - - -
46E ARG* 1.3 71.2 - - - +
48E ILE* 1.4 56.6 + - - +
49E TYR 3.8 14.4 - - - +
50E TYR* 3.5 22.0 - - + -
60E GLY* 3.9 12.3 - - - -
61E ASP* 2.7 47.1 + - - +
62E ILE* 3.0 11.0 + - - +
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Residues in contact with ILE 48 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36E TRP* 2.7 14.5 + - + +
37E TYR* 3.6 24.9 - - - +
38E ARG* 3.8 11.7 - - + +
47E LEU* 1.4 71.9 - - - +
49E TYR* 1.3 58.1 + - + +
60E GLY* 2.7 25.6 + - - -
62E ILE* 3.8 24.9 - - + +
63E ALA* 3.6 13.9 - - - +
66E TYR* 3.5 42.2 - - + -
78E LEU* 3.8 16.6 - - + -
91E TYR* 3.7 30.3 - - + -
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Residues in contact with TYR 49 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35E TYR* 3.7 0.2 - - - -
36E TRP* 2.8 30.6 + - + +
47E LEU* 3.8 2.0 - - - +
48E ILE* 1.3 96.1 - - + +
50E TYR* 1.3 63.4 + - - +
57E PHE* 3.8 22.2 - + - -
58E GLN 3.3 19.7 - - - -
59E LYS* 3.5 47.2 + - + +
60E GLY 4.0 1.1 - - - +
63E ALA* 3.6 16.0 + - + +
66E TYR* 3.6 29.2 + - + -
67E SER* 4.4 4.2 - - - -
68E VAL* 3.4 40.6 - - + -
76E PHE* 3.7 2.7 - - + -
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Residues in contact with TYR 50 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96D GLN* 2.5 35.4 + - - +
97D GLY 3.3 27.4 - - - -
98D ASN* 3.9 10.5 + - + -
34E MET 3.4 4.5 - - - +
35E TYR* 3.3 30.1 - + + -
47E LEU* 3.5 29.2 - - + -
49E TYR* 1.3 77.0 - - - +
51E SER* 1.3 62.3 + - - +
52E GLN* 4.0 6.3 - - + -
57E PHE* 3.4 2.1 - - - +
58E GLN* 2.7 83.0 + - + +
59E LYS 4.0 13.5 - - - -
60E GLY* 4.7 0.2 - - - -
76E PHE* 3.7 5.6 - - - -
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Residues in contact with SER 51 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33E ALA* 3.1 5.4 - - - +
34E MET 2.9 33.7 + - - +
35E TYR* 4.9 0.3 - - - -
50E TYR* 1.3 76.0 - - - +
52E GLN* 1.3 58.6 + - - +
53E ILE 2.9 12.1 + - - -
56E ASP 2.3 30.0 + - - -
57E PHE* 4.2 0.4 - - - +
58E GLN* 5.4 0.4 - - - -
70E ARG* 3.0 22.9 + - - +
76E PHE* 3.6 22.9 - - - -
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Residues in contact with GLN 52 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A ALA* 5.1 5.9 - - - +
4C GLY 3.0 21.4 + - - -
5C LEU* 3.6 0.2 - - - -
6C VAL* 2.8 43.9 + - + +
7C PHE* 6.1 0.2 - - - -
96D GLN 3.3 6.5 + - - -
97D GLY* 3.5 18.0 - - - +
32E ASP* 3.2 23.3 - - - +
33E ALA* 3.8 10.0 - - - +
50E TYR* 4.0 3.6 - - + -
51E SER* 1.3 73.3 + - - +
53E ILE* 1.3 63.0 + - + +
56E ASP* 4.2 5.6 + - - +
58E GLN* 2.9 29.1 + - - +
98E ARG* 5.4 0.2 - - - -
99E SER* 2.8 34.4 + - - +
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Residues in contact with ILE 53 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A ALA* 3.9 12.8 - - - +
72A GLN* 4.1 17.7 - - + +
73A THR* 3.5 24.5 - - - +
76A VAL* 3.9 14.4 - - + -
6C VAL* 4.1 8.1 - - + -
7C PHE 6.0 0.2 - - - -
8C THR* 3.3 34.8 - - + +
32E ASP* 3.5 23.3 + - + +
51E SER* 2.9 18.1 + - - -
52E GLN* 1.3 78.9 - - + +
54E VAL* 1.3 81.1 + - + +
56E ASP* 3.1 20.2 + - + +
70E ARG* 3.9 2.7 - - - -
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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