Contacts of the strand formed by residues 326 - 333 (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 ILE 326 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52F SER 3.6 18.6 - - - +
53F SER* 3.7 5.4 - - - +
54F GLY 3.7 14.4 - - - +
63F ASP 4.4 6.3 - - - +
65F GLY* 3.8 29.4 - - - +
66F LEU 3.3 2.5 - - - -
67F GLN* 3.9 16.4 - - + +
96F THR* 3.8 1.2 + - - +
97F VAL* 3.6 3.6 - - - -
98F LYS* 2.9 53.0 + - + +
100F GLU* 3.6 21.5 - - - +
324F GLY 3.7 10.3 - - - +
325F THR* 1.3 76.8 - - - +
327F PHE* 1.3 66.0 + - - +
328F ASP* 4.2 3.7 + - + +
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Residues in contact with PHE 327 (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 4.5 - - - -
49F PHE* 4.0 24.7 - + - -
65F GLY* 3.2 4.0 - - - -
66F LEU* 2.9 42.7 + - + +
68F THR* 4.6 5.2 - - + -
95F PHE* 4.4 7.2 - + - -
96F THR 3.4 4.3 - - - +
97F VAL* 4.0 16.6 - - + -
107F GLY 4.4 2.2 - - - -
108F GLY* 3.5 38.6 - - - -
109F TYR 5.0 0.2 - - - -
316F LEU* 4.1 22.2 - - + -
318F LEU* 3.9 16.8 - - + -
325F THR* 3.7 27.4 - - + -
326F ILE* 1.3 74.1 - - - +
328F ASP* 1.3 60.8 + - - +
330F PHE* 3.6 19.9 - - + -
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Residues in contact with ASP 328 (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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26F GLN* 3.1 14.4 - - - +
27F PHE* 3.6 7.1 - - - -
62F LYS 3.2 7.4 - - - +
63F ASP* 3.7 11.9 - - - +
64F LYS 3.1 13.4 - - - +
65F GLY* 4.3 2.0 - - - -
95F PHE* 3.8 4.0 - - - +
96F THR* 2.9 38.3 + - - +
326F ILE* 4.2 5.8 + - + +
327F PHE* 1.3 75.5 - - - +
329F ASN* 1.3 95.9 + - - +
330F PHE* 3.2 6.6 + - - -
500F CA 2.3 30.9 - - - -
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Residues in contact with ASN 329 (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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25F GLU 3.2 11.4 + - - -
26F GLN* 3.4 18.6 + - - +
62F LYS 5.2 1.8 + - - +
63F ASP* 5.1 5.1 + - - -
94F GLN* 3.7 3.5 + - - +
95F PHE* 3.5 12.5 + - - -
96F THR* 3.5 22.5 + - + +
169F THR* 5.9 1.0 - - - +
171F LEU* 5.4 1.3 - - + +
328F ASP* 1.3 109.1 + - - +
330F PHE* 1.3 64.3 + - - +
331F LEU* 3.6 1.7 + - - +
342F PHE* 3.9 10.2 - - + -
346F THR* 3.4 46.5 - - + +
347F TRP* 5.5 0.2 - - - +
350F THR* 5.1 1.6 + - - -
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Residues in contact with PHE 330 (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* 4.1 21.5 - + + -
24F LYS* 3.3 9.2 - - - +
25F GLU* 3.0 40.4 + - + +
27F PHE* 3.9 27.8 - + - -
37F TRP* 4.1 8.1 - + - -
66F LEU* 4.7 0.4 - - + -
94F GLN 3.4 7.0 - - - -
95F PHE* 3.6 19.5 - + + -
110F VAL* 3.8 24.0 - - + -
314F LEU* 4.0 27.1 - - + -
316F LEU* 4.0 15.7 - - + -
327F PHE* 3.6 33.7 - - + -
328F ASP 4.1 2.5 - - - -
329F ASN* 1.3 77.3 - - - +
331F LEU* 1.3 59.8 + - - +
342F PHE* 4.1 0.5 - - - -
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Residues in contact with LEU 331 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21F VAL* 4.0 19.3 - - + -
23F PHE 3.3 13.9 - - - +
24F LYS* 4.3 11.0 - - + -
92F VAL 3.7 0.5 - - - +
93F VAL* 3.6 2.1 - - - +
94F GLN* 2.8 46.4 + - + +
329F ASN 4.6 0.4 - - - +
330F PHE* 1.3 76.2 - - - +
332F ILE* 1.3 69.7 + - - +
333F THR* 3.8 18.8 - - + -
338F TYR* 4.1 16.2 - - + -
339F ALA* 3.8 30.5 - - + -
342F PHE* 3.7 30.3 - - + -
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Residues in contact with ILE 332 (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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21F VAL* 3.7 1.9 - - - -
22F TYR* 2.8 29.4 + - + -
23F PHE* 2.8 33.5 + - + +
81F PHE* 4.4 18.8 - - + -
84F PHE* 3.9 16.2 - - + -
91F LEU* 3.8 22.2 - - + -
92F VAL 3.3 10.3 - - - +
93F VAL* 4.7 6.1 - - + -
112F LEU* 4.2 22.2 - - + -
314F LEU* 3.8 27.1 - - + -
331F LEU* 1.3 77.3 - - - +
333F THR* 1.3 64.1 + - - +
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Residues in contact with THR 333 (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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19F PRO 4.9 0.5 - - - -
20F ALA 2.6 23.9 + - - -
21F VAL* 4.5 0.8 - - - -
22F TYR* 4.0 7.6 - - - -
91F LEU* 3.7 7.1 - - - +
92F VAL* 2.8 46.3 + - + +
331F LEU* 3.8 29.8 - - + -
332F ILE* 1.3 75.9 - - - +
334F ASN* 1.3 61.1 + - - +
335F ASP* 3.5 29.2 + - - +
338F TYR* 4.0 13.1 - - + -
339F ALA* 4.2 3.1 - - + +
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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