Contacts of the helix formed by residues 49 - 56 (chain E) in PDB entry 5A15
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 SER 49 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43E LEU 4.6 3.1 + - - -
46E ILE* 2.8 30.1 + - - +
47E PRO 3.1 1.6 - - - -
48E HIS* 1.3 81.0 - - - +
50E LEU* 1.3 59.7 + - - +
51E LEU* 4.0 4.5 + - - +
52E TRP* 3.1 12.5 + - - +
53E LYS* 2.9 28.3 + - - +
89E LEU* 5.7 1.6 - - - +
113E PHE 3.8 0.4 - - - -
114E GLN* 3.6 24.2 - - - -
115E LEU* 3.8 19.2 - - - +
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Residues in contact with LEU 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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49E SER* 1.3 74.6 - - - +
51E LEU* 1.3 63.7 + - - +
53E LYS* 3.1 10.2 + - + +
54E MET* 3.0 46.5 + - + +
112E TYR* 3.2 57.9 - - + +
113E PHE* 3.1 29.8 + - + +
114E GLN* 3.5 20.5 + - - +
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Residues in contact with LEU 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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29E LEU* 5.3 1.8 - - + -
43E LEU* 3.7 27.3 - - + +
49E SER* 3.4 4.8 + - - +
50E LEU* 1.3 78.4 - - - +
52E TRP* 1.3 61.6 + - - +
54E MET* 4.4 11.9 - - - -
55E PHE* 3.2 49.2 + - + +
75E ILE* 5.0 8.1 - - + -
82E PHE* 4.2 20.6 - - + -
85E ILE* 4.9 2.9 - - + -
89E LEU* 3.5 32.8 - - + -
113E PHE* 3.9 34.8 + - + -
115E LEU* 6.0 2.9 - - + -
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Residues in contact with TRP 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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43E LEU 3.6 8.9 + - - +
44E ILE* 3.6 31.4 + - + +
46E ILE 3.3 19.1 - - - +
47E PRO* 3.8 15.5 - - + +
48E HIS* 3.3 51.8 - + - -
49E SER* 3.1 9.9 + - - +
50E LEU 3.1 0.4 - - - -
51E LEU* 1.3 77.4 - - - +
53E LYS* 1.3 81.3 + - + +
56E SER* 2.6 62.3 + - - -
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Residues in contact with LYS 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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48E HIS 5.9 0.4 - - - -
49E SER 2.9 12.5 + - - +
50E LEU* 3.1 17.0 + - + +
52E TRP* 1.3 93.1 - - + +
54E MET* 1.3 61.9 + - + +
56E SER* 4.2 10.3 + - - +
114E GLN* 6.0 0.2 - - - +
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Residues in contact with MET 54 (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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23E PHE* 4.4 8.7 - - - -
50E LEU* 3.0 39.4 + - + +
51E LEU* 3.8 7.4 - - - +
52E TRP 3.2 0.2 - - - -
53E LYS* 1.3 80.9 - - + +
55E PHE* 1.3 85.5 + - + +
56E SER 3.8 3.3 + - - +
65E LEU 4.5 19.0 + - - +
66E ALA 5.8 0.7 - - - +
73E PHE* 6.2 1.8 - - + -
74E PHE 5.2 2.7 - - - +
75E ILE* 3.4 33.4 - - + -
112E TYR* 6.0 1.1 - - - -
113E PHE* 6.1 1.1 - - - -
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Residues in contact with PHE 55 (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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23E PHE* 3.6 33.9 - + - -
27E VAL* 3.9 15.0 - - + -
29E LEU* 3.5 24.7 - - + -
40E HIS* 2.8 40.6 + + + +
43E LEU* 3.7 30.3 - - + -
44E ILE* 4.0 8.7 - - + -
51E LEU* 3.2 38.2 + - + +
52E TRP 3.9 0.4 - - - -
54E MET* 1.3 98.9 - - + +
56E SER* 1.3 62.0 + - - +
57E PRO* 3.6 1.4 - - - +
73E PHE* 4.0 20.0 - + + -
75E ILE* 5.2 0.4 - - + -
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Residues in contact with SER 56 (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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23E PHE* 5.2 1.1 - - - -
44E ILE* 3.9 7.2 - - - +
52E TRP* 2.6 61.6 + - - -
53E LYS* 4.2 10.0 - - - +
54E MET 3.5 3.0 - - - +
55E PHE* 1.3 77.9 - - - +
57E PRO* 1.3 73.1 - - - +
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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