Contacts of the strand formed by residues 21 - 25 (chain A) 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 VAL 21 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A PRO* 3.7 9.1 + - + +
20A ALA* 1.3 76.0 - - - +
22A TYR* 1.3 64.6 + - - +
23A PHE* 4.0 19.1 - - - +
24A LYS* 4.1 20.2 - - + +
331A LEU* 4.0 12.6 - - + -
332A ILE 3.8 2.2 - - - -
333A THR* 4.5 0.9 - - - +
338A TYR* 4.0 28.9 - - + +
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Residues in contact with TYR 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A ALA* 3.7 21.3 - - + +
21A VAL* 1.3 76.1 - - - +
23A PHE* 1.3 61.8 + - + +
81A PHE* 3.4 23.2 - - + +
82A GLU* 4.8 7.3 + - - +
84A PHE* 3.5 69.7 - + + -
89A GLN* 3.1 34.8 + - - -
90A THR 5.3 0.7 - - - -
91A LEU* 5.1 0.7 - - + -
332A ILE* 2.8 21.9 + - + +
333A THR* 4.0 22.7 - - - -
334A ASN* 3.7 8.8 - - + +
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Residues in contact with PHE 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A VAL* 3.4 4.1 - - - -
22A TYR* 1.3 82.2 - - - +
24A LYS* 1.3 70.5 + - - +
25A GLU* 3.9 28.0 - - + -
36A ARG* 6.1 5.8 - - + -
37A TRP* 3.9 12.1 - + - -
79A ALA* 3.6 30.7 - - + -
80A SER 4.3 8.1 - - - -
81A PHE* 3.9 30.3 - + + -
314A LEU* 4.7 12.8 - - + -
330A PHE* 4.1 20.2 - + + -
331A LEU* 3.4 6.6 - - - +
332A ILE* 2.8 49.1 + - + +
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Residues in contact with LYS 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A VAL* 4.1 22.8 - - + +
23A PHE* 1.3 85.2 - - - +
25A GLU* 1.3 66.1 + - - +
26A GLN* 3.6 23.7 - - + +
36A ARG* 5.8 0.7 + - - -
330A PHE 3.4 5.8 - - - +
331A LEU* 4.3 6.1 - - + -
338A TYR* 2.6 30.2 + - - -
342A PHE* 3.5 33.9 - - + -
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Residues in contact with GLU 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A PHE* 3.9 22.3 - - + -
24A LYS* 1.3 76.2 - - - +
26A GLN* 1.3 61.7 + - - +
27A PHE* 3.1 51.5 + - + -
33A TRP* 4.2 0.2 - - - +
36A ARG* 2.9 44.2 + - - +
37A TRP* 2.8 27.7 + - + +
329A ASN* 3.3 6.9 + - - -
330A PHE* 3.0 41.3 + - + +
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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