Contacts of the strand formed by residues 49 - 52 (chain F) in PDB entry 5LK5
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 PHE 49 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33F TRP* 4.3 12.4 - - + -
39F GLU* 5.5 1.9 + - - +
47F GLY 5.2 1.6 - - - -
48F LYS* 1.3 87.0 + - - +
50F VAL* 1.3 64.0 + - - +
66F LEU* 3.6 32.1 - - + -
67F GLN 3.3 17.0 - - - -
68F THR* 3.7 19.3 - - + -
75F TYR* 3.7 33.9 - + + -
76F ALA 4.4 3.1 - - - -
77F LEU* 3.8 40.8 - - + +
316F LEU* 3.8 25.6 - - + -
318F LEU* 5.2 2.7 - - + -
327F PHE* 4.0 21.5 - + - -
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Residues in contact with VAL 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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33F TRP* 4.9 5.4 - - - -
48F LYS* 4.5 15.7 - - + -
49F PHE* 1.3 80.1 - - - +
51F LEU* 1.3 66.6 + - - +
52F SER* 3.5 2.1 + - - -
65F GLY 3.5 0.5 - - - +
66F LEU* 3.7 2.1 - - - -
67F GLN* 2.9 61.3 + - + +
69F SER* 4.0 21.8 - - - +
303J PRO* 4.5 27.8 - - + -
304J SER* 6.0 0.4 - - - +
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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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27F PHE* 3.8 33.0 - - + +
30F GLY* 3.5 28.7 - - - +
31F ASP* 5.1 2.7 - - - +
33F TRP* 3.7 31.7 - - + +
50F VAL* 1.3 73.7 - - - +
52F SER* 1.3 63.8 + - - +
64F LYS* 3.9 26.1 - - + +
65F GLY 3.5 21.3 - - - +
66F LEU* 5.0 1.1 - - + +
303J PRO* 5.1 7.1 - - - +
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Residues in contact with SER 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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50F VAL* 3.5 3.6 + - - -
51F LEU* 1.3 78.5 - - - +
53F SER* 1.3 58.2 + - - +
54F GLY* 3.0 17.2 + - - -
63F ASP 3.8 0.2 - - - +
64F LYS* 3.9 9.6 - - - +
65F GLY 3.0 27.4 + - - +
67F GLN* 3.2 34.6 + - - -
326F ILE* 3.6 10.7 - - - +
303J PRO* 6.2 1.3 - - - -
304J SER* 5.7 0.5 + - - -
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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