Contacts of the strand formed by residues 325 - 333 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66H LEU 3.4 2.1 - - - +
67H GLN* 3.1 4.2 - - - -
68H THR* 3.1 26.5 + - - -
97H VAL* 3.8 10.8 - - + -
98H LYS 3.3 10.3 - - - +
99H HIS* 2.7 37.6 + - + +
101H GLN* 3.0 10.3 + - - +
320H GLN* 2.9 23.5 + - - +
324H GLY* 1.3 75.2 - - - +
326H ILE* 1.3 62.8 + - - +
327H PHE* 3.8 28.2 + - + -
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Residues in contact with ILE 326 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52H SER 3.6 19.5 - - - +
53H SER* 3.8 7.0 - - - +
54H GLY* 3.8 21.5 - - - +
63H ASP 4.4 7.2 - - - +
65H GLY* 3.8 28.5 - - - +
66H LEU 3.3 2.5 - - - +
67H GLN* 3.9 20.4 - - + +
96H THR* 3.8 1.2 + - - +
97H VAL* 3.6 4.0 - - - -
98H LYS* 2.9 52.8 + - + +
100H GLU* 4.4 6.7 - - - +
324H GLY 3.7 9.6 - - - +
325H THR* 1.3 79.2 - - - +
327H PHE* 1.3 64.0 + - - +
328H ASP* 4.2 3.5 + - + +
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Residues in contact with PHE 327 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27H PHE* 3.8 4.5 - - - -
49H PHE* 4.0 24.5 - + - -
65H GLY* 3.2 4.3 - - - -
66H LEU* 2.9 48.9 + - + +
68H THR* 4.5 5.6 - - + -
95H PHE* 4.5 7.9 - + - -
96H THR 3.4 4.7 - - - +
97H VAL* 4.1 16.4 - - + -
107H GLY 4.4 2.0 - - - -
108H GLY* 3.5 39.9 - - - -
109H TYR 4.9 2.9 - - - -
110H VAL* 5.4 1.1 - - + -
316H LEU* 4.4 8.5 - - + -
318H LEU* 3.9 18.6 - - + -
320H GLN* 5.0 0.7 - - - -
325H THR* 3.8 26.2 - - + -
326H ILE* 1.3 73.6 - - - +
328H ASP* 1.3 60.3 + - - +
330H PHE* 3.6 25.8 - + + -
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Residues in contact with ASP 328 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26H GLN* 3.0 14.7 - - - +
27H PHE* 3.5 6.9 - - - -
62H LYS 3.1 8.5 - - - +
63H ASP* 3.7 11.6 - - - +
64H LYS 3.1 12.6 - - - +
65H GLY* 4.3 2.7 - - - -
95H PHE* 3.8 4.0 - - - +
96H THR* 2.9 42.3 + - - +
326H ILE* 4.2 5.3 + - + +
327H PHE* 1.3 73.5 - - - +
329H ASN* 1.3 91.4 + - - +
330H PHE* 3.3 6.9 + - - -
500H CA 2.3 31.3 - - - -
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Residues in contact with ASN 329 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25H GLU 3.3 10.7 + - - -
26H GLN* 3.4 18.4 + - - +
62H LYS 5.2 2.0 + - - +
63H ASP* 5.1 5.1 + - - -
94H GLN* 3.7 4.0 + - - +
95H PHE* 3.6 11.4 - - - -
96H THR* 3.5 21.8 + - + +
171H LEU* 5.5 1.3 - - + +
328H ASP* 1.3 108.7 + - - +
330H PHE* 1.3 64.6 + - - +
331H LEU* 3.6 1.4 + - - +
342H PHE* 3.9 9.6 - - + -
346H THR* 3.4 47.0 - - + +
350H THR* 5.2 1.6 + - - -
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Residues in contact with PHE 330 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23H PHE* 4.1 21.3 - + + -
24H LYS* 3.3 9.4 - - - +
25H GLU* 3.0 40.8 + - + +
27H PHE* 3.9 29.4 - + - -
37H TRP* 4.1 8.7 - + - -
66H LEU* 4.7 0.7 - - + -
94H GLN 3.4 7.0 - - - -
95H PHE* 3.6 20.2 - + + -
110H VAL* 3.8 23.8 - - + -
314H LEU* 4.0 26.7 - - + -
316H LEU* 4.1 14.4 - - + -
327H PHE* 3.6 33.2 - - + -
328H ASP 4.1 2.9 - - - -
329H ASN* 1.3 77.7 - - - +
331H LEU* 1.3 59.0 + - - +
342H PHE* 4.1 0.9 - - - -
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Residues in contact with LEU 331 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21H VAL* 4.0 19.5 - - + -
23H PHE 3.3 14.6 - - - +
24H LYS* 4.3 11.7 - - + -
92H VAL 3.7 2.3 - - - +
94H GLN* 2.8 47.0 + - + +
329H ASN 4.6 0.4 - - - +
330H PHE* 1.3 75.9 - - - +
332H ILE* 1.3 69.4 + - - +
333H THR* 3.9 18.4 - - + -
338H TYR* 4.1 15.9 - - + -
339H ALA* 3.8 29.8 - - + -
342H PHE* 3.7 31.0 - - + -
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Residues in contact with ILE 332 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21H VAL* 3.6 1.9 - - - -
22H TYR* 2.8 34.3 + - + -
23H PHE* 2.8 36.0 + - + +
81H PHE* 4.5 10.8 - - + -
84H PHE* 3.9 17.0 - - + -
91H LEU* 3.8 22.0 - - + -
92H VAL 3.3 10.8 - - - +
93H VAL* 4.7 5.6 - - + -
112H LEU* 3.4 35.7 - - + -
314H LEU* 3.8 16.4 - - + -
331H LEU* 1.3 79.2 - - - +
333H THR* 1.3 60.3 + - - +
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Residues in contact with THR 333 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19H PRO 4.9 0.3 - - - -
20H ALA 2.6 23.9 + - - -
21H VAL* 4.5 0.8 - - - -
22H TYR* 4.0 6.5 - - - -
91H LEU* 3.7 7.8 - - - +
92H VAL* 2.8 45.6 + - + +
331H LEU* 3.9 31.0 - - + -
332H ILE* 1.3 75.3 - - - +
334H ASN* 1.3 63.2 + - - +
335H ASP* 3.4 29.3 + - - +
338H TYR* 4.0 13.0 - - + -
339H ALA* 4.1 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