Contacts of the strand formed by residues 325 - 333 (chain D) 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 THR 325 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66D LEU 3.4 2.1 - - - +
67D GLN* 3.1 3.8 - - - -
68D THR* 3.0 26.6 + - - -
97D VAL* 3.9 10.8 - - + -
98D LYS 3.3 10.3 - - - +
99D HIS* 2.7 38.5 + - + +
101D GLN* 3.0 10.6 + - - +
320D GLN* 2.9 24.2 + - - +
324D GLY* 1.3 75.3 - - - +
326D ILE* 1.3 63.6 + - - +
327D PHE* 3.7 29.4 + - + -
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Residues in contact with ILE 326 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52D SER 3.5 20.0 - - - +
53D SER* 3.8 5.8 - - - +
54D GLY 3.8 13.7 - - - +
63D ASP 4.4 6.7 - - - +
65D GLY* 3.8 28.7 - - - +
66D LEU 3.3 2.2 - - - -
67D GLN* 3.9 16.2 - - + +
96D THR* 3.8 1.4 + - - +
97D VAL* 3.6 3.6 - - - -
98D LYS* 2.9 50.7 + - + +
100D GLU* 3.6 21.3 - - - +
324D GLY 3.7 10.5 - - - +
325D THR* 1.3 77.0 - - - +
327D PHE* 1.3 65.7 + - - +
328D ASP* 4.1 4.1 + - + +
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Residues in contact with PHE 327 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D PHE* 3.8 5.0 - - - -
49D PHE* 4.0 25.6 - + - -
65D GLY* 3.2 4.0 - - - -
66D LEU* 2.9 42.9 + - + +
68D THR* 4.5 4.9 - - + -
95D PHE* 4.5 6.5 - + - -
96D THR 3.4 4.5 - - - +
97D VAL* 4.1 17.7 - - + -
107D GLY 4.4 1.8 - - - -
108D GLY* 3.5 37.9 - - - -
109D TYR 5.0 0.2 - - - -
316D LEU* 4.1 22.2 - - + -
318D LEU* 3.9 15.9 - - + -
320D GLN* 5.0 0.2 - - - -
325D THR* 3.7 27.4 - - + -
326D ILE* 1.3 73.9 - - - +
328D ASP* 1.3 60.1 + - - +
330D PHE* 3.6 19.7 - - + -
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Residues in contact with ASP 328 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26D GLN* 3.0 14.6 - - - +
27D PHE* 3.6 5.8 - - - -
62D LYS 3.2 8.3 - - - +
63D ASP* 3.7 11.6 - - - +
64D LYS 3.1 12.2 - - - +
65D GLY* 4.4 2.0 - - - -
95D PHE* 3.8 4.0 - - - +
96D THR* 2.9 41.0 + - - +
326D ILE* 4.1 5.6 + - + +
327D PHE* 1.3 75.2 - - - +
329D ASN* 1.3 92.5 + - - +
330D PHE* 3.3 7.4 + - - -
500D CA 2.3 31.3 - - - -
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Residues in contact with ASN 329 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D GLU 3.2 10.9 + - - -
26D GLN* 3.4 28.6 + - - +
62D LYS 5.2 2.1 + - - +
63D ASP* 5.1 5.3 + - - -
94D GLN* 3.7 3.8 + - - +
95D PHE* 3.5 11.6 - - - -
96D THR* 3.6 21.6 + - + +
171D LEU* 5.5 1.5 - - + +
328D ASP* 1.3 108.9 + - - +
330D PHE* 1.3 64.4 + - - +
331D LEU* 3.6 1.7 + - - +
342D PHE* 3.9 9.7 - - + -
346D THR* 3.4 36.6 - - + +
350D THR* 5.1 1.6 + - - -
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Residues in contact with PHE 330 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D PHE* 4.1 20.4 - + + -
24D LYS* 3.4 8.5 - - - +
25D GLU* 3.0 41.6 + - + +
27D PHE* 3.9 26.9 - + - -
37D TRP* 4.1 7.6 - + - -
66D LEU* 4.7 0.7 - - + -
94D GLN 3.4 6.5 - - - -
95D PHE* 3.6 19.5 - + + -
110D VAL* 3.8 24.0 - - + -
314D LEU* 4.0 26.5 - - + -
316D LEU* 4.1 16.2 - - + -
327D PHE* 3.6 32.8 - - + -
328D ASP 4.0 4.0 - - - -
329D ASN* 1.3 77.6 - - - +
331D LEU* 1.3 60.5 - - - +
342D PHE* 4.1 0.3 - - - -
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Residues in contact with LEU 331 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D VAL* 4.0 19.1 - - + -
23D PHE 3.3 14.4 - - - +
24D LYS* 4.3 11.2 - - + -
92D VAL 3.6 2.1 - - - +
94D GLN* 2.8 47.5 + - + +
329D ASN 4.5 0.9 - - - +
330D PHE* 1.3 75.5 - - - +
332D ILE* 1.3 70.5 + - - +
333D THR* 3.8 19.1 - - + -
338D TYR* 4.1 16.2 - - + -
339D ALA* 3.8 29.8 - - + -
342D PHE* 3.7 30.5 - - + -
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Residues in contact with ILE 332 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D VAL* 3.7 1.6 - - - -
22D TYR* 2.8 29.4 + - + -
23D PHE* 2.8 38.9 + - + +
81D PHE* 4.4 10.5 - - + -
84D PHE* 3.9 17.3 - - + -
91D LEU* 3.8 22.0 - - + -
92D VAL 3.3 9.6 - - - +
93D VAL* 4.7 6.5 - - + -
112D LEU* 3.4 35.4 - - + -
314D LEU* 3.8 16.4 - - + -
331D LEU* 1.3 77.3 - - - +
333D THR* 1.3 64.3 + - - +
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Residues in contact with THR 333 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D PRO* 4.4 1.0 - - - +
20D ALA 2.7 23.1 + - - -
21D VAL* 4.7 0.4 - - - -
22D TYR* 4.0 6.9 - - - -
91D LEU* 3.7 7.6 - - - +
92D VAL* 2.8 46.0 + - + +
331D LEU* 3.8 31.0 - - + -
332D ILE* 1.3 76.2 - - - +
334D ASN* 1.3 62.6 + - - +
335D ASP* 3.5 28.5 + - - +
338D TYR* 4.0 13.0 - - + -
339D ALA* 4.2 3.6 - - + +
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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