Contacts of the strand formed by residues 330 - 336 (chain B) in PDB entry 3K3B
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 330 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18B ASN 2.8 27.8 + - - +
19B ILE* 3.1 18.1 - - + +
20B GLN* 2.8 16.1 + - - +
89B ILE* 5.0 0.4 - - - -
100B THR* 3.4 7.9 - - - +
102B PHE* 4.0 18.8 - - + -
299B ILE* 4.2 12.8 - - + -
323B SER 3.6 4.5 + - - -
324B LEU* 3.5 35.9 + - + +
328B THR* 3.5 13.7 + - - -
329B ARG* 1.3 73.9 - - - +
331B SER* 1.3 64.3 + - - +
332B ILE* 4.8 2.5 - - + -
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Residues in contact with SER 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B GLN* 3.3 18.4 + - - +
22B VAL* 4.7 4.2 - - - +
85B VAL* 3.3 22.1 - - - +
89B ILE* 3.5 26.2 - - - -
100B THR 3.0 8.4 + - - +
101B ILE* 3.2 5.9 - - - +
102B PHE* 2.7 34.0 + - - +
330B THR* 1.3 76.2 - - - +
332B ILE* 1.3 62.6 + - - +
333B ILE* 4.1 3.2 - - - +
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Residues in contact with ILE 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B ILE* 4.1 6.1 - - + -
20B GLN 3.0 6.2 + - - +
21B VAL* 3.6 26.2 - - + +
22B VAL* 3.0 28.2 + - - +
102B PHE* 3.8 31.4 - - + -
104B TYR* 4.2 21.3 - - + -
266B LEU* 5.6 0.9 - - + -
295B LEU* 6.2 2.2 - - + -
299B ILE* 3.7 40.8 - - + -
330B THR* 4.8 1.8 - - + -
331B SER* 1.3 76.5 + - - +
333B ILE* 1.3 64.5 + - - +
334B ALA* 3.7 4.6 + - + +
352B TYR* 5.5 8.7 - - + -
353B ALA* 6.4 1.8 - - + -
356B ALA* 4.6 5.8 - - + -
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Residues in contact with ILE 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B VAL* 3.6 24.9 - - + -
24B ARG* 4.0 27.4 - - + +
72B PHE* 5.7 0.4 - - + -
81B VAL* 4.2 11.9 - - + -
85B VAL* 4.3 7.6 - - + -
101B ILE* 4.1 11.4 - - + -
102B PHE 2.9 16.7 + - - +
103B ALA* 3.4 3.9 - - - -
104B TYR 2.8 31.7 + - - +
114B THR* 3.7 16.6 - - + -
115B MET* 5.1 0.9 - - + -
135B ILE* 3.6 30.5 - - + -
331B SER* 4.4 7.4 - - - +
332B ILE* 1.3 72.7 - - - +
334B ALA* 1.3 56.0 + - - +
335B THR* 3.5 12.7 + - + +
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Residues in contact with ALA 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B VAL* 5.3 1.3 - - + -
22B VAL 2.9 15.3 + - - +
23B VAL* 3.2 18.2 - - + +
24B ARG 3.0 21.6 + - - -
104B TYR* 3.2 12.8 - - + -
332B ILE* 3.7 4.9 + - + +
333B ILE* 1.3 70.2 - - - +
335B THR* 1.3 60.9 + - - +
349B THR* 3.9 19.7 - - + +
350B LEU* 5.6 0.2 - - + -
353B ALA* 4.0 23.8 - - + -
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Residues in contact with THR 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B ARG* 3.1 13.0 - - + +
103B ALA* 5.3 0.7 - - + -
104B TYR 2.7 16.9 + - - +
105B GLY* 3.7 4.7 - - - -
109B THR* 2.7 42.0 + - - +
110B GLY 4.0 20.2 - - - +
111B LYS* 3.5 17.0 + - + +
114B THR* 4.1 7.6 - - - +
333B ILE* 4.1 22.9 - - + +
334B ALA* 1.3 74.7 - - - +
336B ILE* 1.3 65.5 + - - +
349B THR* 3.6 10.2 + - - +
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Residues in contact with ILE 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B VAL* 3.8 20.4 - - + -
24B ARG 3.0 3.1 + - - +
25B CYS* 3.4 18.1 - - + -
26B ARG* 3.0 29.8 + - - +
41B VAL* 3.7 31.0 - - + -
43B CYS* 5.0 0.2 - - - -
50B VAL* 4.2 10.3 - - + -
109B THR* 3.8 10.0 - - - -
334B ALA 4.4 3.1 - - - +
335B THR* 1.3 81.1 - - - +
337B SER* 1.3 60.0 + - - +
346B THR* 3.8 29.4 - - + +
349B THR* 3.7 24.7 - - + -
350B LEU* 4.2 9.9 - - + -
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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