Contacts of the helix formed by residues 49 - 56 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43F LEU 4.5 4.2 + - - -
46F ILE* 2.7 28.6 + - - +
47F PRO 3.1 1.4 - - - -
48F HIS* 1.3 81.7 - - - +
50F LEU* 1.3 60.4 + - - +
51F LEU* 4.0 3.3 + - - +
52F TRP* 3.1 14.1 + - - +
53F LYS* 2.9 28.2 + - - +
89F LEU* 5.6 2.1 - - - +
113F PHE 4.0 4.0 - - - -
114F GLN* 3.6 24.5 - - - -
115F LEU* 4.1 13.8 - - - +
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Residues in contact with LEU 50 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49F SER* 1.3 75.1 - - - +
51F LEU* 1.3 64.5 + - + +
53F LYS* 3.2 17.0 + - + +
54F MET* 3.2 29.3 + - + +
112F TYR* 3.1 55.0 - - + +
113F PHE* 3.2 22.9 + - + +
114F GLN* 3.1 28.1 + - - +
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Residues in contact with LEU 51 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43F LEU* 3.7 28.5 - - + +
49F SER* 3.4 3.5 + - - +
50F LEU* 1.3 80.4 - - + +
52F TRP* 1.3 62.7 + - - +
54F MET* 4.7 6.1 - - - +
55F PHE* 3.4 45.0 + - + +
75F ILE* 4.7 13.7 - - + -
82F PHE* 4.3 19.7 - - + -
85F ILE* 4.7 2.9 - - + -
89F LEU* 3.6 30.7 - - + -
113F PHE* 3.8 38.9 + - + -
115F LEU* 6.1 1.1 - - + -
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Residues in contact with TRP 52 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43F LEU 3.7 6.0 + - - -
44F ILE* 3.3 34.2 + - + +
46F ILE 3.3 4.9 - - - +
47F PRO* 3.7 24.6 - - + +
48F HIS* 3.2 42.6 - + - -
49F SER* 3.1 23.7 + - - +
50F LEU 3.1 0.2 - - - -
51F LEU* 1.3 79.4 - - - +
53F LYS* 1.3 78.2 + - + +
56F SER* 2.5 61.0 + - - -
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Residues in contact with LYS 53 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48F HIS 6.0 0.2 - - - -
49F SER 2.9 13.1 + - - +
50F LEU* 3.2 15.0 + - + +
52F TRP* 1.3 93.6 - - + +
54F MET* 1.3 60.6 + - + +
56F SER* 4.1 11.2 - - - +
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Residues in contact with MET 54 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23F PHE* 5.4 2.9 - - - -
50F LEU* 3.2 31.2 + - + +
51F LEU* 4.0 5.8 - - - +
52F TRP 3.2 0.4 - - - -
53F LYS* 1.3 80.9 - - + +
55F PHE* 1.3 81.2 + - + +
56F SER 3.4 3.3 + - - +
65F LEU* 3.6 49.0 - - + +
73F PHE* 6.0 3.1 - - + -
74F PHE 5.0 4.3 - - - +
75F ILE* 3.7 31.4 - - + -
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Residues in contact with PHE 55 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23F PHE* 4.2 22.6 - + - -
27F VAL* 3.9 21.5 - - + -
29F LEU* 5.9 5.2 - - + -
40F HIS* 2.9 45.6 + + + +
43F LEU* 3.7 31.0 - - + -
44F ILE* 4.1 7.9 - - + -
51F LEU* 3.4 27.3 + - + +
52F TRP 3.9 0.2 - - - -
54F MET* 1.3 107.1 - - + +
56F SER* 1.3 61.9 + - - +
57F PRO* 3.7 3.3 - - - +
65F LEU* 5.2 3.6 - - + -
73F PHE* 4.1 31.6 - + + -
75F ILE* 5.2 4.5 - - + -
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Residues in contact with SER 56 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23F PHE* 6.2 0.2 - - - -
44F ILE* 3.7 8.5 - - - +
52F TRP* 2.5 61.1 + - - -
53F LYS* 4.1 11.1 - - - +
54F MET 3.4 3.8 - - - +
55F PHE* 1.3 77.4 - - - +
57F PRO* 1.4 75.0 - - - +
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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